MALDIquantForeign/0000755000175000017500000000000012615440675015005 5ustar sebastiansebastianMALDIquantForeign/NAMESPACE0000644000175000017500000000205712615214352016217 0ustar sebastiansebastian# Generated by roxygen2: do not edit by hand export(import) export(importAnalyze) export(importBrukerFlex) export(importCdf) export(importCiphergenXml) export(importCsv) export(importImzMl) export(importMsd) export(importMzMl) export(importMzXml) export(importTab) export(importTxt) export(supportedFileFormats) exportMethods(export) exportMethods(exportCsv) exportMethods(exportImzMl) exportMethods(exportMsd) exportMethods(exportMzMl) exportMethods(exportTab) import(MALDIquant) import(methods) import(readMzXmlData) importFrom(XML,xmlEventParse) importFrom(XML,xmlParse) importFrom(XML,xmlValue) importFrom(XML,xpathApply) importFrom(XML,xpathSApply) importFrom(base64enc,base64encode) importFrom(digest,digest) importFrom(readBrukerFlexData,readBrukerFlexFile) importFrom(stats,na.omit) importFrom(stats,runif) importFrom(utils,download.file) importFrom(utils,modifyList) importFrom(utils,packageVersion) importFrom(utils,read.table) importFrom(utils,tail) importFrom(utils,type.convert) importFrom(utils,untar) importFrom(utils,unzip) importFrom(utils,write.table) MALDIquantForeign/R/0000755000175000017500000000000012615214412015172 5ustar sebastiansebastianMALDIquantForeign/R/createMassObject-functions.R0000644000175000017500000000644212615211441022546 0ustar sebastiansebastian## Copyright 2014-2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Create a MassSpectrum or a MassPeaks object. #' #' This function creates a MassSpectrum or MassPeaks object (depending on the #' centroided argument). #' #' @param mass mass data #' @param intensity intensity data #' @param snr snr data #' @param metaData \code{list}, metaData #' @param centroided \code{logical}, centroided #' (if TRUE => MassPeaks, if FALSE => MassSpectrum) #' @param massRange \code{double}, length == 2, trim spectrum to #' \code{massRange}. #' @param minIntensity \code{double}, minimal intensity #' @param verbose \code{logical}, verbose output? #' #' @return Returns a MassSpectrum or a MassPeaks object. #' #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @rdname createMassObject #' @keywords internal #' @noRd .createMassObject <- function(mass, intensity, snr=NULL, metaData=list(), centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE) { if (!is.null(metaData$centroided) || !is.null(metaData$dataProcessing$centroided)) { isCentroided <- isTRUE(as.logical(as.numeric(metaData$centroided))) | isTRUE(as.logical(as.numeric(metaData$dataProcessing$centroided))) if (isCentroided != centroided) { warning("According to the metadata information the imported data are ", ifelse(isCentroided, "", "not "), "centroided, ", "but they are treated as ", ifelse(centroided, "centroided (MassPeaks)", "profile (MassSpectrum)"), " data. Maybe you want to use ", sQuote(paste0("centroided=", as.character(isCentroided))), ". See ", sQuote("?import"), " for details.", immediate.=TRUE) } } .msg(centroided & verbose, "Assume centroided data and creating a MassPeaks object.") ## trim AbstractMass object massRange <- MALDIquant:::.reorderRange(massRange) ## we don't use MALDIquant::trim here because we want to filter on the ## intensity as well i <- which(massRange[1L] <= mass & mass <= massRange[2L] & intensity >= minIntensity) if (is.null(snr)) { snr <- rep.int(NA_real_, length(i)) } ## create a MassPeaks object for centroided data if (centroided) { m <- createMassPeaks(mass=mass[i], intensity=intensity[i], snr=snr[i], metaData=metaData) } else { m <- createMassSpectrum(mass=mass[i], intensity=intensity[i], metaData=metaData) } m } MALDIquantForeign/R/package.R0000644000175000017500000000331412615214341016712 0ustar sebastiansebastian## Copyright 2012-2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Import/Export routines for MALDIquant #' #' This package reads and writes different file formats of mass #' spectrometry data into/from MALDIquant objects. #' #' \tabular{ll}{ #' Package: \tab MALDIquantForeign \cr #' License: \tab GPL (>= 3)\cr #' URL: \tab http://strimmerlab.org/software/maldiquant/\cr #' } #' #' @docType package #' @name MALDIquantForeign-package #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @keywords package #' #' @import MALDIquant #' @import readMzXmlData #' @import methods #' @importFrom base64enc base64encode #' @importFrom digest digest #' @importFrom readBrukerFlexData readBrukerFlexFile #' @importFrom stats na.omit runif #' @importFrom utils download.file modifyList packageVersion read.table tail #' type.convert write.table untar unzip #' @importFrom XML xmlEventParse xmlParse xmlValue xpathApply xpathSApply #' NULL MALDIquantForeign/R/list.files-functions.R0000644000175000017500000000337012523634201021402 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .list.files <- function(path, pattern, excludePattern=NULL, recursive=TRUE, ignore.case=TRUE) { files <- list.files(path=path, pattern=pattern, recursive=recursive, ignore.case=ignore.case, full.names=TRUE) if (!is.null(excludePattern)) { isExcluded <- grepl(pattern=excludePattern, x=files, ignore.case=ignore.case) files <- files[!isExcluded] } normalizePath(files) } .files <- function(path, pattern, excludePattern=NULL, ignore.case=TRUE, ...) { isDir <- file.info(path)$isdir files <- normalizePath(path[!isDir]) isMatching <- unlist(regexpr(pattern=pattern, text=basename(files), ignore.case=ignore.case)) != -1 files <- files[isMatching] files <- c(files, .list.files(path=path[isDir], pattern=pattern, excludePattern=excludePattern, ignore.case=ignore.case, ...)) unique(files) } MALDIquantForeign/R/export-functions.R0000644000175000017500000000503712523634201020651 0ustar sebastiansebastian## Copyright 2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .exportToFile <- function(x, file, type="auto", force=FALSE, ...) { if (file.exists(file) && !force) { stop("File already exists! Use ", sQuote("force=TRUE"), " to overwrite it.") } if (missing(type) || pmatch(tolower(type), "auto", nomatch=0, duplicates.ok=FALSE)) { type <- .fileExtension(file) } i <- pmatch(tolower(type), exportFormats$type, nomatch=0, duplicates.ok=FALSE) if (i) { handler <- exportFormats$handler[i] return(do.call(handler, list(x=x, file=file, ...))) } else { stop("File type ", sQuote(type), " is not supported!") } } .exportToDir <- function(x, path, type, force=FALSE, ...) { if (!file.exists(path) && force) { dir.create(path, showWarnings=FALSE, recursive=TRUE) } if (!file.exists(path)) { stop("Directory ", sQuote(path), " doesn't exist!") } if (!file.info(path)$isdir) { stop(sQuote(path), " is no directory!") } ## stop if directory isn't writeable if (file.access(path, 2) != 0) { stop("No permissions to write into ", sQuote(path), "!") } i <- pmatch(tolower(type), exportFormats$type, nomatch=0, duplicates.ok=FALSE) if (i) { filenames <- .composeFilename(x, fileExtension=exportFormats$extension[i]) filenames <- file.path(path, filenames) optArgs <- list(...) peaks <- list() if (hasArg(peaks)) { peaks <- optArgs$peaks optArgs$peaks <- NULL } for (i in seq(along=x)) { arguments <- list(x=x[[i]], file=filenames[i], type=type, force=force) arguments <- modifyList(arguments, optArgs) if (length(peaks)) { arguments$peaks <- peaks[[i]] } do.call(export, arguments) } } else { stop("File type ", sQuote(type), " is not supported!") } invisible() } MALDIquantForeign/R/exportMsd-methods.R0000644000175000017500000000171612523634201020750 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see setMethod(f=".exportMsd", signature=signature(x="MassSpectrum"), definition=function(x, file, peaks, ...) { return(.writeMsdDocument(x=x, file=file, peaks=peaks, ...)) }) MALDIquantForeign/R/importAuto-functions.R0000644000175000017500000000410512523634201021466 0ustar sebastiansebastian## Copyright 2012-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importAuto <- function(path, excludePattern=NULL, removeEmptySpectra=TRUE, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE, ...) { files <- lapply(importFormats$pattern, .files, path=path, excludePattern=excludePattern) names(files) <- importFormats$type ## test xml files for ciphergen format files$ciphergen <- .testCiphergenXml(files$ciphergen) n <- vapply(files, length, integer(1)) if (all(n)) { stop("Could not detect any supported file type.") } m <- which.max(n) .msg(verbose, n[m], " files of type=", sQuote(importFormats$type[m]), " found.") import(path=files[[m]], type=importFormats$type[m], pattern=importFormats$pattern[m], removeEmptySpectra=removeEmptySpectra, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose, ...) } # test xml for ciphergen format # returns files in ciphergen xml format .testCiphergenXml <- function(files) { ## read first 4 lines of each file l <- lapply(files, readLines, n=4) p <- lapply(l, grepl, pattern="||") s <- vapply(p, sum, integer(1)) isCiphergen <- s >= 2 files[isCiphergen] } MALDIquantForeign/R/importTab-functions.R0000644000175000017500000000507412601026330021265 0ustar sebastiansebastian## Copyright 2012-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importTab <- function(file, centroided=FALSE, massRange=c(0L, Inf), minIntensity=0L, skip=0L, sep=.autoSep(file, skip=skip), header=.autoHeader(file, sep=sep, skip=skip), verbose=FALSE, ...) { ## load ms file s <- read.table(file=file, header=header, sep=sep, skip=skip, stringsAsFactors=FALSE, ...) list(.createMassObject(mass=s[, 1L], intensity=s[, 2L], metaData=list(file=file), centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose)) } .importCsv <- function(file, centroided=FALSE, massRange=c(0L, Inf), minIntensity=0L, skip=0L, sep=.autoSep(file, skip=skip), header=.autoHeader(file, sep=sep, skip=skip), verbose=FALSE, ...) { .importTab(file=file, centroided=centroided, massRange=massRange, minIntensity=minIntensity, skip=skip, sep=sep, header=header, verbose=verbose, ...) } .autoHeader <- function(file, sep="\t", skip=0L) { l <- tail(readLines(file, n=skip+1L), 1L) l <- gsub(pattern='[\\\\"]*', replacement="", x=l) l <- strsplit(l, split=sep)[[1L]][1L] !is.numeric(type.convert(l, as.is=TRUE)) } .autoSep <- function(file, sep=c(",", ";", "\t", " "), skip=0L) { l <- tail(readLines(file, n=skip+1L), 1L) pattern <- paste0(".+", sep, ".+") i <- vapply(pattern, function(x) { g <- gregexpr(pattern=x, text=l)[[1L]] return(all(g > 0L) & length(g) == 1L) }, logical(1L)) if (any(i)) { return(sep[which(i)[1L]]) ## return only first match } else { return(sep[1L]) } } MALDIquantForeign/R/mzMl-functions.R0000644000175000017500000004216212523634201020247 0ustar sebastiansebastian## Copyright 2013-2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .writeMzMlDocument <- function(x, file, id, encoding="utf-8", imsArgs=list()) { ## stop if file isn't writeable if (file.exists(file) && file.access(file, 2) != 0) { stop("No permissions to write into ", sQuote(file), "!") } isIms <- length(imsArgs) ## file handle f <- file(file, open="wt", encoding=encoding) .writeXmlHeader(file=f, encoding=encoding) .writeXmlTag("mzML", attrs=c(xmlns="http://psi.hupo.org/ms/mzml", "xmlns:xsi"="http://www.w3.org/2001/XMLSchema-instance", "xsi:schemaLocation"=paste("http://psi.hupo.org/ms/mzml", "http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd"), id=.sanitize(ifelse(missing(id) || is.null(id), deparse(substitute(x)), id)), version="1.1.0"), close=FALSE, file=f) .writeMzMlCvList(file=f, isIms=isIms) .writeMzMlFileDescription(x, file=f, isIms=isIms, imsArgs=imsArgs) .writeMzMlSoftwareList(x, file=f) if (isIms) { .writeImzMlReferenceableParamGroups(x, file=f) .writeImzMlScanSettings(x, file=f) } .writeMzMlInstrumentConfigurationList(x, file=f) .writeMzMlDataProcessingList(x, file=f) .writeMzMlRun(x, file=f, isIms=isIms) .writeCloseXmlTag("mzML", file=f) invisible(close(f)) } .writeMzMlCvList <- function(file, isIms=FALSE) { items <- list( ms=list(id="MS", fullName="Proteomics Standards Initiative Mass Spectrometry Ontology", version="3.44.0", URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"), uo=list(id="UO", fullName="Unit Ontology", version="12:10:2012", URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo")) if (isIms) { items$imzml <- list(id="IMS", fullName="Imaging MS Ontology", version="0.9.1", URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo") } .writeXmlTag("cvList", attrs=c(count=2), intend=1, close=FALSE, file=file) for (i in seq(along=items)) { .writeXmlTag("cv", attrs=items[[i]], intend=2, file=file) } .writeCloseXmlTag("cvList", intend=1, file=file) } .writeMzMlFileDescription <- function(x, file, isIms=FALSE, imsArgs) { .writeXmlTag("fileDescription", intend=1, close=FALSE, file=file) .writeXmlTag("fileContent", intend=2, close=FALSE, file=file) .writeXmlTag("cvParam", intend=3, attrs=c(cvRef="MS", accession="MS:1000579", name="MS1 spectrum"), file=file) if (isIms) { .writeXmlTag("cvParam", intend=3, attrs=c(cvRef="IMS", accession="IMS:1000080", name="universally unique identifier", value=paste0("{", imsArgs$uuid, "}")), file=file) .writeXmlTag("cvParam", intend=3, attrs=c(cvRef="IMS", accession="IMS:1000091", name="ibd SHA-1", value=imsArgs$sha1), file=file) if (imsArgs$processed) { .writeXmlTag("cvParam", intend=3, attrs=c(cvRef="IMS", accession="IMS:1000031", name="processed"), file=file) } else { .writeXmlTag("cvParam", intend=3, attrs=c(cvRef="IMS", accession="IMS:1000030", name="continuous"), file=file) } } .writeXmlTag("userParam", intend=3, attrs=c(name="MALDIquantForeign", value="MALDIquant object(s) exported to mzML"), file=file) .writeCloseXmlTag("fileContent", intend=2, file=file) .writeMzMlSourceFileList(x, file=file) .writeCloseXmlTag("fileDescription", intend=1, file=file) } .writeMzMlSourceFileList <- function(x, file) { files <- unique(unlist(lapply(x, function(s)metaData(s)$file))) if (length(files)) { dname <- dirname(files) bname <- basename(files) ext <- tolower(.fileExtension(bname)) .writeXmlTag("sourceFileList", attrs=c(count=length(files)), intend=2, close=FALSE, file=file) for (i in seq(along=files)) { .writeXmlTag("sourceFile", intend=3, attrs=c(id=paste0("SF", i), location=dname[i], name=bname[i]), close=FALSE, file=file) if (ext[i] == "fid") { .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000825", name="Bruker FID file"), file=file) .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000773", name="Bruker FID nativeID format"), file=file) } else if (ext[i] == "mzxml") { .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000566", name="ISB mzXML file"), file=file) } else if (ext[i] == "mzml") { .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000584", name="mzML file"), file=file) } if (file.exists(files[i])) { .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000569", name="SHA-1", value=digest::digest(files[i], algo="sha1", file=TRUE)), file=file) } .writeCloseXmlTag("sourceFile", intend=3, file=file) } .writeCloseXmlTag("sourceFileList", intend=2, file=file) } } .writeMzMlSoftwareList <- function(x, file) { .writeXmlTag("softwareList", attrs=c(count=1), intend=1, close=FALSE, file=file) .writeXmlTag("software", intend=2, attrs=c(id="MALDIquantForeign", version=as.character(packageVersion("MALDIquantForeign"))), file=file) .writeCloseXmlTag("softwareList", intend=1, file=file) } .writeMzMlInstrumentConfigurationList <- function(x, file) { .writeXmlTag("instrumentConfigurationList", attrs=c(count=1), intend=1, close=FALSE, file=file) .writeXmlTag("instrumentConfiguration", attrs=c(id="IC0"), intend=2, file=file) .writeCloseXmlTag("instrumentConfigurationList", intend=1, file=file) } .writeMzMlDataProcessingList <- function(x, file) { .writeXmlTag("dataProcessingList", attrs=c(count=1), intend=1, close=FALSE, file=file) .writeXmlTag("dataProcessing", attrs=c(id="export"), intend=2, close=FALSE, file=file) .writeXmlTag("processingMethod", intend=3, attrs=c(order=1, softwareRef="MALDIquantForeign"), close=FALSE, file=file) .writeXmlTag("userParam", intend=4, attrs=c(name="MALDIquant object(s) exported to mzML", value=""), file=file) .writeCloseXmlTag("processingMethod", intend=3, file=file) .writeCloseXmlTag("dataProcessing", intend=2, file=file) .writeCloseXmlTag("dataProcessingList", intend=1, file=file) } .writeMzMlRun <- function(x, file, isIms=FALSE) { .writeXmlTag("run", attrs=c(id="run0", defaultInstrumentConfigurationRef="IC0"), intend=1, close=FALSE, file=file) .writeMzMlSpectrumList(x, file=file, isIms=isIms) .writeCloseXmlTag("run", intend=1, file=file) } .writeMzMlSpectrumList <- function(x, file, isIms=FALSE) { .writeXmlTag("spectrumList", attrs=c(count=length(x), defaultDataProcessingRef="export"), intend=2, close=FALSE, file=file) for (i in seq(along=x)) { id <- ifelse(is.null(metaData(x[[i]])$id), paste0("scan=", i-1L), metaData(x[[i]])$id) .writeXmlTag("spectrum", intend=3, attrs=c(index=i-1, id=id, defaultArrayLength=length(x[[i]]), spotID=metaData(x[[i]])$fullName), close=FALSE, file=file) msLevel <- ifelse(is.null(metaData(x[[i]])$msLevel), 1, metaData(x[[i]])$msLevel) .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000511", name="ms level", value=msLevel), file=file) .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000294", name="mass spectrum"), file=file) .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000528", name="lowest observed m/z", value=min(mass(x[[i]])), unitCvRef="MS", unitAccession="MS:1000040", unitName="m/z"), file=file) .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000527", name="highest observed m/z", value=max(mass(x[[i]])), unitCvRef="MS", unitAccession="MS:1000040", unitName="m/z"), file=file) .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000285", name="total ion current", value=totalIonCurrent(x[[i]])), file=file) if (MALDIquant::isMassSpectrum(x[[i]])) { .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000128", name="profile spectrum"), file=file) } else { .writeXmlTag("cvParam", intend=4, attrs=c(cvRef="MS", accession="MS:1000127", name="centroid spectrum"), file=file) } if (isIms) { .writeImzMlScanList(x[[i]], file=file) .writeImzMlBinaryDataArrayList(x[[i]], file=file) } else { .writeMzMlBinaryDataArrayList(x[[i]], file=file) } .writeCloseXmlTag("spectrum", intend=3, file=file) } .writeCloseXmlTag("spectrumList", intend=2, file=file) } .writeMzMlBinaryDataArrayList <- function(x, file) { count <- ifelse(MALDIquant::isMassSpectrum(x), 2, 3) .writeXmlTag("binaryDataArrayList", attrs=c(count=count), intend=4, close=FALSE, file=file) .writeMzMlBinaryData(mass(x), file=file, c(cvRef="MS", accession="MS:1000514", name="m/z array", unitCvRef="MS", unitAccession="MS:1000040", unitName="m/z")) .writeMzMlBinaryData(intensity(x), file=file, c(cvRef="MS", accession="MS:1000515", name="intensity array", unitCvRef="MS", unitAccession="MS:1000131", unitName="number of counts")) if (MALDIquant::isMassPeaks(x)) { .writeMzMlBinaryData(snr(x), file=file, c(cvRef="MS", accession="MS:1000517", name="signal to noise array")) } .writeCloseXmlTag("binaryDataArrayList", intend=4, file=file) } .writeMzMlBinaryData <- function(x, file, additionalAttrs) { binaryData <- .base64encode(x, size=8, endian="little", compressionType="gzip") .writeXmlTag("binaryDataArray", attrs=c(encodedLength=nchar(binaryData)), intend=5, close=FALSE, file=file) .writeXmlTag("cvParam", intend=6, file=file, attrs=c(cvRef="MS", accession="MS:1000574", name="zlib compression")) .writeXmlTag("cvParam", intend=6, file=file, attrs=c(cvRef="MS", accession="MS:1000523", name="64-bit float")) if (!missing(additionalAttrs)) { .writeXmlTag("cvParam", attrs=additionalAttrs, intend=6, file=file) } .writeXmlTag("binary", text=binaryData, intend=6, file=file) .writeCloseXmlTag("binaryDataArray", intend=5, file=file) } .writeImzMlReferenceableParamGroups <- function(x, file) { .writeXmlTag("referenceableParamGroupList", attrs=c(count=2), intend=1, close=FALSE, file=file) .writeXmlTag("referenceableParamGroup", attrs=c(id="mzArray"), intend=2, close=FALSE, file=file) .writeXmlTag("cvParam", intend=3, file=file, attrs=c(cvRef="MS", accession="MS:1000514", name="m/z array", unitCvRef="MS", unitAccession="MS:1000040", unitName="m/z")) ref <- c("MS", "MS", "IMS") accession <- paste(ref, c(1000576, 1000523, 1000101), sep=":") name <- c("no compression", "64-bit float", "external data") value <- c("", "", "true") for (i in seq(along=accession)) { .writeXmlTag("cvParam", intend=3, file=file, attrs=c(cvRef=ref[i], accession=accession[i], name=name[i], value=value[i])) } .writeCloseXmlTag("referenceableParamGroup", intend=2, file=file) .writeXmlTag("referenceableParamGroup", attrs=c(id="intensityArray"), intend=2, close=FALSE, file=file) .writeXmlTag("cvParam", intend=3, file=file, attrs=c(cvRef="MS", accession="MS:1000515", name="intensity array", unitCvRef="MS", unitAccession="MS:1000131")) for (i in seq(along=accession)) { .writeXmlTag("cvParam", intend=3, file=file, attrs=c(cvRef=ref[i], accession=accession[i], name=name[i], value=value[i])) } .writeCloseXmlTag("referenceableParamGroup", intend=2, file=file) .writeCloseXmlTag("referenceableParamGroupList", intend=1, file=file) } .writeImzMlScanSettings <- function(x, file) { .writeXmlTag("scanSettingsList", attrs=c(count=1), intend=1, close=FALSE, file=file) .writeXmlTag("scanSettings", attrs=c(id="scansetting1"), intend=2, close=FALSE, file=file) accession <- paste("IMS", 1000042:1000043, sep=":") name <- paste("max count of pixel", c("x", "y")) value <- unname(metaData(x[[1L]])$imaging$size) for (i in seq(along=accession)) { .writeXmlTag("cvParam", intend=3, file=file, attrs=c(cvRef="IMS", accession=accession[i], name=name[i], value=value[i])) } accession <- paste("IMS", 1000044:1000047, sep=":") name <- c(paste("max dimension", c("x", "y")), paste("pixel size", c("x", "y"))) value <- unname(c(metaData(x[[1L]])$imaging$dim, metaData(x[[1L]])$imaging$pixelSize)) for (i in seq(along=accession)) { .writeXmlTag("cvParam", intend=3, file=file, attrs=c(cvRef="IMS", accession=accession[i], name=name[i], value=value[i], unitCvRef="UO", unitAccession="UO:0000017", unitName="micrometer")) } .writeCloseXmlTag("scanSettings", intend=2, file=file) .writeCloseXmlTag("scanSettingsList", intend=1, file=file) } .writeImzMlScanList <- function(x, file) { .writeXmlTag("scanList", attrs=c(count=1), intend=4, close=FALSE, file=file) .writeXmlTag("scan", intend=5, close=FALSE, file=file) accession <- paste("IMS", 1000050:1000051, sep=":") name <- paste("position", c("x", "y")) value <- unname(metaData(x)$imaging$pos) for (i in seq(along=accession)) { .writeXmlTag("cvParam", intend=6, file=file, attrs=c(cvRef="IMS", accession=accession[i], name=name[i], value=value[i])) } .writeCloseXmlTag("scan", intend=5, file=file) .writeCloseXmlTag("scanList", intend=4, file=file) } .writeImzMlBinaryDataArrayList <- function(x, file) { .writeXmlTag("binaryDataArrayList", attrs=c(count=2), intend=4, close=FALSE, file=file) .writeImzMlBinaryData(metaData(x)$imaging$offsets["mass",], file=file, ref="mzArray") .writeImzMlBinaryData(metaData(x)$imaging$offsets["intensity",], file=file, ref="intensityArray") .writeCloseXmlTag("binaryDataArrayList", intend=4, file=file) } .writeImzMlBinaryData <- function(x, file, ref) { .writeXmlTag("binaryDataArray", attrs=c(encodedLength=0), intend=5, close=FALSE, file=file) .writeXmlTag("referenceableParamGroupRef", attrs=c(ref=ref), intend=6, file=file) accession <- paste("IMS", 1000102:1000104, sep=":") name <- paste("external", c("offset", "array length", "encoded length")) value <- unname(x) for (i in seq(along=accession)) { .writeXmlTag("cvParam", intend=6, file=file, attrs=c(cvRef="IMS", accession=accession[i], name=name[i], value=value[i])) } .writeXmlTag("binary", intend=6, file=file) .writeCloseXmlTag("binaryDataArray", intend=5, file=file) } MALDIquantForeign/R/AllGenerics.R0000644000175000017500000000420312523634201017504 0ustar sebastiansebastian## Copyright 2012-2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see if (is.null(getGeneric(".composeFilename"))) setGeneric(".composeFilename", function(x, ...) standardGeneric(".composeFilename")) if (is.null(getGeneric(".exportTab"))) setGeneric(".exportTab", function(x, ...) standardGeneric(".exportTab")) if (is.null(getGeneric(".exportCsv"))) setGeneric(".exportCsv", function(x, ...) standardGeneric(".exportCsv")) if (is.null(getGeneric(".exportImzMl"))) setGeneric(".exportImzMl", function(x, ...) standardGeneric(".exportImzMl")) if (is.null(getGeneric(".exportMsd"))) setGeneric(".exportMsd", function(x, ...) standardGeneric(".exportMsd")) if (is.null(getGeneric(".exportMzMl"))) setGeneric(".exportMzMl", function(x, ...) standardGeneric(".exportMzMl")) if (is.null(getGeneric("export"))) setGeneric("export", function(x, ...) standardGeneric("export")) if (is.null(getGeneric("exportTab"))) setGeneric("exportTab", function(x, ...) standardGeneric("exportTab")) if (is.null(getGeneric("exportCsv"))) setGeneric("exportCsv", function(x, ...) standardGeneric("exportCsv")) if (is.null(getGeneric("exportImzMl"))) setGeneric("exportImzMl", function(x, ...) standardGeneric("exportImzMl")) if (is.null(getGeneric("exportMsd"))) setGeneric("exportMsd", function(x, ...) standardGeneric("exportMsd")) if (is.null(getGeneric("exportMzMl"))) setGeneric("exportMzMl", function(x, ...) standardGeneric("exportMzMl")) MALDIquantForeign/R/importAnalyze-functions.R0000644000175000017500000000433512601026330022161 0ustar sebastiansebastian## Copyright 2013-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importAnalyze <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE) { header <- .readAnalyzeHdr(file, verbose=verbose) mass <- .readAnalyzeMass(.changeFileExtension(file, "t2m"), header=header, verbose=verbose) massRange <- MALDIquant:::.reorderRange(massRange) massIdx <- which(massRange[1] <= mass & mass <= massRange[2]) skip <- c(massIdx[1]-1, length(mass)-massIdx[length(massIdx)]) mass <- mass[massIdx] intensity <- .readAnalyzeIntensity(.changeFileExtension(file, "img"), header=header, ni=length(mass), skip=skip, verbose=verbose) l <- vector(mode="list", length=header$nx*header$ny) for (x in 1:header$nx) { for (y in 1:header$ny) { l[[(x-1)*header$ny+y]] <- .createMassObject(mass=mass, intensity=intensity[, x, y], metaData=list(file=file, imaging=list(pos=c(x=x, y=y), pixelSize=c(x=header$xd, y=header$yd))), centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose) } } l } MALDIquantForeign/R/fileFormats.R0000644000175000017500000000777312523634201017606 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Supported file formats #' #' This function prints all file formats supported by #' \code{\link{MALDIquantForeign-package}}. #' #' \subsection{Import}{ #' #' \tabular{ll}{ #' txt \tab \code{\link[MALDIquantForeign]{importTxt}} \cr #' tab \tab \code{\link[MALDIquantForeign]{importTab}} \cr #' csv \tab \code{\link[MALDIquantForeign]{importCsv}} \cr #' fid \tab \code{\link[MALDIquantForeign]{importBrukerFlex}} \cr #' ciphergen \tab \code{\link[MALDIquantForeign]{importCiphergenXml}} \cr #' mzXML \tab \code{\link[MALDIquantForeign]{importMzXml}} \cr #' mzML \tab \code{\link[MALDIquantForeign]{importMzMl}} \cr #' imzML \tab \code{\link[MALDIquantForeign]{importImzMl}} \cr #' analyze \tab \code{\link[MALDIquantForeign]{importAnalyze}} \cr #' cdf \tab \code{\link[MALDIquantForeign]{importCdf}} \cr #' msd \tab \code{\link[MALDIquantForeign]{importMsd}} \cr #' } #' } #' #' \subsection{Export}{ #' #' \tabular{ll}{ #' tab \tab \code{\link[MALDIquantForeign]{exportTab}} \cr #' csv \tab \code{\link[MALDIquantForeign]{exportCsv}} \cr #' imzML \tab \code{\link[MALDIquantForeign]{exportImzMl}} \cr #' msd \tab \code{\link[MALDIquantForeign]{exportMsd}} \cr #' mzML \tab \code{\link[MALDIquantForeign]{exportMzMl}} \cr #' } #' } #' #' @return a \code{list} with two named elements (\code{import} and #' \code{export}) containing a \code{character} vector of supported file types. #' #' @seealso #' \code{\link[MALDIquantForeign]{export}}, #' \code{\link[MALDIquantForeign]{import}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' library("MALDIquantForeign") #' #' supportedFileFormats() #' #' @rdname supportedFileFormats-functions #' @export supportedFileFormats <- function() { list(import=importFormats$type, export=exportFormats$type) } importFormats <- data.frame(type=c("txt", "tab", "csv", "fid", "ciphergen", "mzxml", "mzml", "imzml", "analyze", "cdf", "msd"), pattern=c("^.*\\.txt$", "^.*\\.tab$", "^.*\\.csv$", "^fid$", "^.*\\.xml$", "^.*\\.mzXML$", "^.*\\.mzML$", "^.*\\.imzML$", "^.*\\.hdr$", "^.*\\.cdf$", "^.*\\.msd$"), handler=c(rep(".importTab", 2), ".importCsv", ".importBrukerFlex", ".importCiphergenXml", ".importMzXml", ".importMzMl", ".importImzMl", ".importAnalyze", ".importCdf", ".importMsd"), stringsAsFactors=FALSE) exportFormats <- data.frame(type=c("tab", "csv", "msd", "mzml", "imzml"), extension=c("tab", "csv", "msd", "mzML", "imzML"), onefile=c(FALSE, FALSE, FALSE, TRUE, TRUE), handler=c(".exportTab", ".exportCsv", ".exportMsd", ".exportMzMl", ".exportImzMl"), stringsAsFactors=FALSE) MALDIquantForeign/R/filename-methods.R0000644000175000017500000000373412523634201020545 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' This method creates a filename for a \code{\linkS4class{AbstractMassObject}} #' object. #' #' @param x a \code{\linkS4class{AbstractMassObject}} object #' @param fileExtension file type (e.g. "txt", "pdf", ...) #' @return filename #' #' @seealso \code{\linkS4class{AbstractMassObject}} #' @aliases .composeFilename,AbstractMassObject-method #' @aliases .composeFilename,list-method #' @docType methods #' @keywords internal #' @noRd setMethod(f=".composeFilename", signature=signature(x="AbstractMassObject"), definition=function(x, fileExtension="csv") { if (!is.null(metaData(x)$fullName)) { if (length(metaData(x)$fullName) > 1) { filename <- paste0(metaData(x)$fullName, collapse="_") } else { filename <- metaData(x)$fullName } } else { filename <- .withoutFileExtension(metaData(x)$file[1]) } filename <- paste(filename, fileExtension, sep=".") return(filename) }) setMethod(f=".composeFilename", signature=signature(x="list"), definition=function(x, fileExtension="csv") { stopifnot(MALDIquant:::.isMassObjectList(x)) filenames <- unlist(lapply(x, .composeFilename, fileExtension=fileExtension)) .uniqueBaseFilenames(filenames, fileExtension) }) MALDIquantForeign/R/analyze-functions.R0000644000175000017500000001127612523634201020775 0ustar sebastiansebastian## Copyright 2013-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see ## Analyze 7.5 header file .readAnalyzeHdr <- function(filename, verbose=FALSE) { if (!file.exists(filename)) { stop(sQuote(filename), " isn't readable.") } size <- file.info(filename)$size ## Analyze 7.5 header must be of size 348; ABSciex files are a little bit ## larger (384) if (size != 348 && size != 384) { stop(sQuote(filename), " is no ANALYZE header file.") } .msg(verbose, "Extracting header information from ", sQuote(filename), " ...") f <- file(filename, open="rb") on.exit(close(f)) ## first 4 bytes have to be 348 in little endian mode ## (384 for ABSciex) endian <- ifelse(readBin(f, "integer", n=1, size=4, endian="little") %in% c(348, 384), "little", "big") ## skip unused entries seek(f, where=38) regular <- readChar(f, nchars=1, useBytes=TRUE) if (regular != "r") { stop("Wrong file format. Images have to be of equal size (", sQuote("regular"), " must be ", sQuote("r"), ")") } ## skip unused entries seek(f, where=40) ## 2 == number of intensity, 3 == ncol (x), 4 == nrow (y) ## use as.double() here to avoid integer overflows in calculations like nx*ny ## later ## Thanks to Ken Frankel for reporting this problem. dimensions <- as.double(readBin(f, "integer", n=8, size=2, endian=endian)) ## We use the size of the t2m file. See .readAnalyzeIntensity for details. #ni <- dimensions[2] nx <- dimensions[3] ny <- dimensions[4] ## skip unused entries seek(f, where=70) datatype <- readBin(f, "integer", n=1, size=2, endian=endian) bitpix <- readBin(f, "integer", n=1, size=2, endian=endian) if (datatype %in% c(2, 4, 8)) { what <- "integer" } else if (datatype %in% c(16, 32, 64)) { what <- "double" } else { what <- "raw" } signed <- datatype == 2 size <- bitpix/8 ## skip unused entries seek(f, where=76) pixdim <- readBin(f, "double", n=8, size=4, endian=endian) ## pixelwidth in mm xd <- pixdim[2] yd <- pixdim[3] return(list(nx=nx, ny=ny, xd=xd, yd=yd, endian=endian, what=what, signed=signed, size=size)) } ## Analyze 7.5 img file .readAnalyzeIntensity <- function(filename, header, ni, skip=c(0, 0), verbose=FALSE) { if (!file.exists(filename)) { stop(sQuote(filename), " isn't readable.") } .msg(verbose, "Reading intensity values from ", sQuote(filename), " ...") stopifnot(length(skip) == 2) skip <- skip*header$size f <- file(filename, open="rb") on.exit(close(f)) ## header$ni should contain the number of intensity values ## because the format specification uses int16 for header$ni it is limited to ## 32767 intensity values. ## We use the size of the t2m file divided by 4 to find the correct number to ## circumvent this size limit. ## Thanks to Ken Frankel for reporting this problem. i <- vector(mode=header$what, length=ni*header$nx*header$ny) dim(i) <- c(ni, header$nx, header$ny) for (y in 1:header$ny) { for (x in 1:header$nx) { ## CAUTION: seek on Windows is possibly buggy; see ?seek for details. ## If there are any bug reports on Windows we maybe have to ignore "skip" ## on Windows (which would disable the mass range/memory saving feature ## completely). seek(f, where=seek(f)+skip[1]) i[, x, y] <- readBin(f, what=header$what, n=ni, size=header$size, signed=header$signed, endian=header$endian) seek(f, where=seek(f)+skip[2]) } } return(i) } ## Analyze 7.5 t2m file .readAnalyzeMass <- function(filename, header, verbose=FALSE) { if (!file.exists(filename)) { stop(sQuote(filename), " isn't readable.") } .msg(verbose, "Reading mass values from ", sQuote(filename), " ...") n <- file.info(filename)$size/4 f <- file(filename, open="rb") on.exit(close(f)) m <- readBin(f, what="double", n=n, size=4, signed=TRUE, endian=header$endian) return(m) } MALDIquantForeign/R/importMzMl-functions.R0000644000175000017500000000267712601030514021443 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importMzMl <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE) { .msg(verbose, "Reading spectrum from ", sQuote(file), " ...") if (!file.exists(file)) { stop("File ", sQuote(file), " doesn't exists!") } s <- .parseMzMl(file=file, verbose=verbose) lapply(s$spectra, function(x, globalS=s) { m <- modifyList(s$metaData, x$metaData) m$file <- file .createMassObject(mass=x$mass, intensity=x$intensity, snr=x$snr, metaData=m, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose) }) } MALDIquantForeign/R/testChecksum-functions.R0000644000175000017500000000247512523634201021775 0ustar sebastiansebastian## Copyright 2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .testChecksum <- function(file, target, algo="sha1", ..., verbose=FALSE) { .msg(verbose, "Calculating ", algo, "-sum for ", sQuote(file), ": ", appendLF=FALSE) fileChecksum <- tolower(digest::digest(file, algo=algo, file=TRUE, ...)) target <- tolower(target) .msg(verbose, fileChecksum) if (fileChecksum != target) { warning("Stored and calculated ", algo, " sums do not match ", "(stored: ", sQuote(target), ", calculated: ", sQuote(fileChecksum), ")!") return(FALSE) } return(TRUE) } MALDIquantForeign/R/importMzXml-functions.R0000644000175000017500000000303412601030514021617 0ustar sebastiansebastian## Copyright 2012-2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importMzXml <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE, ...) { l <- readMzXmlData:::.readMzXmlFile(mzXmlFile=file, verbose=verbose, ...) lapply(l, function(x).createMassObject(mass=x$spectrum$mass, intensity=x$spectrum$intensity, snr=x$spectrum$snr, metaData=x$metaData, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose)) } MALDIquantForeign/R/xml-functions.R0000644000175000017500000000307212523634201020125 0ustar sebastiansebastian## Copyright 2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .writeXmlHeader <- function(file, encoding) { cat("\n", file=file, sep="") } .writeCloseXmlTag <- function(tag, intend=0, file) { cat(paste0(rep(" ", times=intend)), "\n", file=file, sep="", append=TRUE) } .writeXmlTag <- function(tag, text=NULL, attrs=NULL, intend=0, close=TRUE, file) { intend <- paste0(rep(" ", times=intend)) if (length(attrs)) { attrs <- paste0(" ", names(attrs), "=\"", attrs, "\"") } if (length(text)) { text <- paste0(">", text) if (close) { text <- paste0(text, "") } } else { text <- ">" if (close) { text <- "/>" } } cat(intend, "<", tag, attrs, text, "\n", file=file, sep="", append=TRUE) } MALDIquantForeign/R/importMsd-functions.R0000644000175000017500000000262112601026330021275 0ustar sebastiansebastian## Copyright 2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importMsd <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE) { .msg(verbose, "Reading spectrum from ", sQuote(file), " ...") if (!file.exists(file)) { stop("File ", sQuote(file), " doesn't exists!") } ## read file s <- .parseMsd(file=file, verbose=verbose) s$metaData$file <- file list(.createMassObject(mass=s$spectrum$mass, intensity=s$spectrum$intensity, metaData=s$metaData, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose)) } MALDIquantForeign/R/parseMsd.R0000644000175000017500000001067612615213136017107 0ustar sebastiansebastian## Copyright 2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Parse msd files. #' #' This function parses msd files. #' #' @param file \code{character}, path to msd file. #' @param verbose \code{logical}, verbose output? #' #' @return Returns a list with metadata and spectra. #' #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @keywords internal #' @noRd .parseMsd <- function(file, verbose=FALSE, ...) { XML::xmlEventParse(file=file, handlers=.msdHandlers(fileName=file, verbose=verbose), addContext=FALSE, useTagName=TRUE, useDotNames=TRUE, ...)$getData() } #' Parse msd files. #' #' This function is defines handlers for XML SAX parser. Internal use only. #' #' @param fileName \code{character}, path to msd file #' @param verbose \code{logical}, verbose output? #' #' @return function closure #' #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @references mMass homepage: \url{http://mmass.org/} #' @keywords internal #' @noRd .msdHandlers <- function(fileName, verbose=FALSE) { ## define local variables ## handle different mzXML versions msdVersion <- 0 ## save last opened tag (needed for .text()-processing) text <- character() endian <- "little" precision <- 32 ## build final list xml <- list() xml$metaData <- list() xml$spectrum <- list() ## handlers for specific tags ## mSD mSD <- function(name, attrs) { ## fetch version information msdVersion <<- readMzXmlData:::.grepDouble(attrs["version"]) .msg(verbose, "Found mSD document (version: ", msdVersion, ").") } ## mSD/description/date date <- function(name, attrs) { xml$metaData[["acquisitionDate"]] <<- readMzXmlData:::.attributeToString(attrs, "value") } operator <- function(name, attrs) { xml$metaData[["owner"]] <<- readMzXmlData:::.attributeToString(attrs, "value") } institution <- function(name, attrs) { xml$metaData[[name]] <<- readMzXmlData:::.attributeToString(attrs, "value") } ## mSD/spectrum spectrum <- function(name, attrs) { attributeNames <- c("scanNumber", "msLevel", "retentionTime", "precursorMZ", "precursorCharge", "polarity") attributeNames <- intersect(attributeNames, names(attrs)) for (i in attributeNames) { xml$metaData[[i]] <<- readMzXmlData:::.attributeToDouble(attrs, i) } } ## mSD/spectrum/mzArray mzArray <- function(name, attrs) { precision <<- readMzXmlData:::.attributeToDouble(attrs, "precision") endian <<- readMzXmlData:::.attributeToString(attrs, "endian") } ## default functions to catch tags without a handler .endElement <- function(name, attrs) { if (name == "title") { xml$metaData[c("name", "fullName", "sampleName")] <<- text } else if (name == "notes") { xml$metaData[["comment"]] <<- text } else if (name == "mzArray") { xml$spectrum[["mass"]] <<- .decodeArray() } else if (name == "intArray") { xml$spectrum[["intensity"]] <<- .decodeArray() } text <<- character() } .text <- function(x) { text <<- paste0(text, x) } .decodeArray <- function() { readMzXmlData:::.base64decode(x=text, endian=endian, size=round(precision/8L), compressionType="gzip") } ## return statement (please call getData()) return(list(getData=function() {return(xml)}, mSD=mSD, date=date, institution=institution, instrument=institution, spectrum=spectrum, mzArray=mzArray, intArray=mzArray, .endElement=.endElement, .text=.text)) } MALDIquantForeign/R/parseMzMl.R0000644000175000017500000003045012615214070017231 0ustar sebastiansebastian## Copyright 2012-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Parse mzML files. #' #' This function parses mzML files. #' #' @param file \code{character}, path to mzML file #' @param verbose \code{logical}, verbose output? #' #' @return Returns a list with metadata and spectra. #' #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @keywords internal #' @noRd .parseMzMl <- function(file, verbose=FALSE, ...) { XML::xmlEventParse(file=file, handlers=.mzMlHandlers(fileName=file, verbose=verbose), addContext=FALSE, useTagName=TRUE, useDotNames=TRUE, ...)$getData() } #' Parse mzML files. #' #' This function is defines handlers for XML SAX parser. Internal use only. #' #' TODO: fetch obo map file and use it #' #' @param fileName \code{character}, path to mzML file #' @param verbose \code{logical}, verbose output? #' #' @return function closure #' #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @references #' Definition of \code{mzML} format: #' \url{http://www.psidev.info/mzml_1_0_0} #' @keywords internal #' @noRd .mzMlHandlers <- function(fileName, verbose=FALSE) { ## define local variables ## handle different mzXML versions mzMlVersion <- 0 ## save last opened tag (needed for .text()-processing) openTag <- "" ## store current scan values nSpectra <- 0L curSpecIdx <- 0L curRefId <- character() currentArrayContent <- character() fileCheckSum <- character() ## supported? supported <- TRUE ## build final list xml <- list() xml$metaData <- list() xml$spectra <- list() ## imzML information xml$ims <- list() ## reference values references <- new.env(parent=emptyenv()) ## handlers for specific tags ## mzML mzML <- function(name, attrs) { ## fetch version information mzMlVersion <<- readMzXmlData:::.grepDouble(attrs["xsi:schemaLocation"]) .msg(verbose, "Found mzML document (version: ", mzMlVersion, ").") } ## mzML/referenceableParamGroupList/referenceableParamGroup referenceableParamGroup <- function(name, attrs) { openTag <<- name curRefId <<- readMzXmlData:::.attributeToString(attrs, "id", required=TRUE) } referenceableParamGroupRef <- function(name, attrs) { if (!is.null(references[[attrs["ref"]]])) { xml$spectra[[curSpecIdx]]$metaData <<- modifyList(xml$spectra[[curSpecIdx]]$metaData, references[[attrs["ref"]]]) } } ## mzML/run/spectrumList spectrumList <- function(name, attrs) { ## fetch number of spectra nSpectra <<- readMzXmlData:::.attributeToDouble(attrs, "count", required=TRUE) .msg(verbose, "Found ", nSpectra, " ", ifelse(nSpectra == 1, "spectrum", "spectra"), ".") } ## mzML/run/spectrumList/spectrum spectrum <- function(name, attrs) { openTag <<- name curSpecIdx <<- curSpecIdx + 1 supported <<- TRUE xml$spectra[[curSpecIdx]] <<- list() xml$spectra[[curSpecIdx]]$metaData <<- list() xml$spectra[[curSpecIdx]]$metaData[["id"]] <<- readMzXmlData:::.attributeToString(attrs, "id", required=TRUE) xml$spectra[[curSpecIdx]]$metaData[["numberInFile"]] <<- curSpecIdx ## IMS extension if (length(xml$ims)) { xml$ims$ibd[[curSpecIdx]] <<- matrix(NA, nrow=2, ncol=3, dimnames=list(c("mass", "intensity"), c("offset", "length", "encodedLength"))) xml$spectra[[curSpecIdx]]$metaData$imaging <<- list() } .msg(verbose, "Processing spectrum ", curSpecIdx, "/", nSpectra, " (id: ", attrs["id"], ") ...") } chromatogram <- function(name, attrs) { warning(" tag is not supported!") supported <<- FALSE } ## *cvParam cvParam <- function(name, attrs) { ## polarity if (.isAttrSet(attrs, "MS:1000129", "negative scan")) { .setCvValue("negative", "polarity") return() } else if (.isAttrSet(attrs, "MS:1000130", "positive scan")) { .setCvValue("positive", "polarity") return() } ## ms level if (.isAttrSet(attrs, "MS:1000511", "ms level")) { .setCvValue( readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE), "msLevel") return() } ## centroid data if (.isAttrSet(attrs, "MS:1000127", "centroid spectrum")) { .setCvValue(1, "centroided") return() } ## precision if (.isAttrSet(attrs, "MS:1000521", "32-bit float")) { .setCvValue(32, "precision") return() } else if (.isAttrSet(attrs, "MS:1000523", "64-bit float")) { .setCvValue(64, "precision") return() } ## compression if (.isAttrSet(attrs, "MS:1000576", "no compression")) { .setCvValue("none", "compressionType") return() } else if (.isAttrSet(attrs, "MS:1000574", "zlib compression")) { .setCvValue("gzip", "compressionType") return() } ## data arrays if (.isAttrSet(attrs, "MS:1000514", "m/z array")) { .setCvValue("mass", "currentArray") return() } else if (.isAttrSet(attrs, "MS:1000515", "intensity array")) { .setCvValue("intensity", "currentArray") return() } else if (.isAttrSet(attrs, "MS:1000517", "signal to noise array")) { .setCvValue("snr", "currentArray") return() } ## IMS extensions if (.isAttrSet(attrs, "IMS:1000080", "universally unique identifier")) { xml$ims$uuid <<- gsub(pattern="[[:punct:]]", replacement="", x=readMzXmlData:::.attributeToString(attrs, "value", required=TRUE)) return() } if (.isAttrSet(attrs, "IMS:1000090", "ibd MD5")) { xml$ims$md5 <<- readMzXmlData:::.attributeToString(attrs, "value") return() } if (.isAttrSet(attrs, "IMS:1000091", "ibd SHA-1")) { xml$ims$sha1 <<- readMzXmlData:::.attributeToString(attrs, "value") return() } if (.isAttrSet(attrs, "IMS:1000030", "continuous")) { xml$ims$type <<- "continuous" return() } if (.isAttrSet(attrs, "IMS:1000031", "processed")) { xml$ims$type <<- "processed" return() } if (.isAttrSet(attrs, "IMS:1000042", "max count of pixel x")) { xml$metaData$imaging$size["x"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000043", "max count of pixel y")) { xml$metaData$imaging$size["y"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000044", "max dimension x")) { xml$metaData$imaging$dim["x"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000045", "max dimension y")) { xml$metaData$imaging$dim["y"]<<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000046", "pixel size x")) { xml$metaData$imaging$pixelSize["x"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000047", "pixel size y")) { xml$metaData$imaging$pixelSize["y"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000050", "position x")) { xml$spectra[[curSpecIdx]]$metaData$imaging$pos["x"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000051", "position y")) { xml$spectra[[curSpecIdx]]$metaData$imaging$pos["y"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000102", "external offset")) { xml$ims$ibd[[curSpecIdx]][xml$spectra[[curSpecIdx]]$metaData$currentArray, "offset"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000103", "external array length")) { xml$ims$ibd[[curSpecIdx]][xml$spectra[[curSpecIdx]]$metaData$currentArray, "length"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } if (.isAttrSet(attrs, "IMS:1000104", "external encoded length")) { xml$ims$ibd[[curSpecIdx]][xml$spectra[[curSpecIdx]]$metaData$currentArray, "encodedLength"] <<- readMzXmlData:::.attributeToDouble(attrs, "value", required=TRUE) return() } } ## default functions to catch tags without a handler .startElement <- function(name, attrs) { openTag <<- name } .endElement <- function(name, attrs) { if (name == "binary" && supported) { .decodeArray() } else if (name == "fileChecksum") { .calculateFileChecksum() } if (openTag == name) { openTag <<- "" } } .text <- function(x) { if (openTag == "binary" && supported) { currentArrayContent <<- paste0(currentArrayContent, x) } else if (openTag == "fileChecksum") { fileCheckSum <<- paste0(fileCheckSum, x) } } ## helper functions .isAttrSet <- function(attrs, id, name) { return(attrs["accession"] == id || attrs["name"] == name) } .setCvValue <- function(x, name) { if (openTag == "referenceableParamGroup") { if (is.null(references[[curRefId]])) { references[[curRefId]] <<- list() } references[[curRefId]][[name]] <<- x } else if (openTag == "spectrum" || openTag == "binaryDataArray") { xml$spectra[[curSpecIdx]]$metaData[[name]] <<- x } else { xml$metaData[[name]] <<- x } } .decodeArray <- function() { if (length(currentArrayContent)) { ## read base64 encoded array content (endian must be "little") content <- readMzXmlData:::.base64decode(x=currentArrayContent, endian="little", size=round(xml$spectra[[curSpecIdx]]$metaData$precision/8), compressionType=xml$spectra[[curSpecIdx]]$metaData$compressionType) xml$spectra[[curSpecIdx]][[xml$spectra[[curSpecIdx]]$metaData$currentArray]] <<- content ## clear array content currentArrayContent <<- character() } ## clear metaData xml$spectra[[curSpecIdx]]$metaData[c("precision", "compressionType", "currentArray")] <<- NULL } .calculateFileChecksum <- function() { n <- nchar(fileCheckSum) if (n <= 0) { return() } ## sha1 sum for this file (from the beginning of the file up to (and ## including) the opening tag .msg(verbose, "Look for '' position ...") ## 14 == nchar("") checkSumPos <- readMzXmlData:::.revfregexpr("", fileName) + 14 .testChecksum(fileName, fileCheckSum, algo="sha1", length=checkSumPos-1, verbose=verbose) } ## return statement (please call getData()) return(list(getData=function() {return(xml)}, mzML=mzML, referenceableParamGroup=referenceableParamGroup, referenceableParamGroupRef=referenceableParamGroupRef, spectrumList=spectrumList, spectrum=spectrum, chromatogram=chromatogram, cvParam=cvParam, .startElement=.startElement, .endElement=.endElement, .text=.text)) } MALDIquantForeign/R/sanitize-functions.R0000644000175000017500000000172512523634201021156 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .sanitize <- function(x) { x <- gsub(pattern="&", replacement="&", x=x) x <- gsub(pattern="<", replacement="<", x=x) x <- gsub(pattern=">", replacement=">", x=x) x } MALDIquantForeign/R/importBrukerFlex-functions.R0000644000175000017500000000247412601026330022631 0ustar sebastiansebastian## Copyright 2012-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importBrukerFlex <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE, ...) { s <- readBrukerFlexData::readBrukerFlexFile(fidFile=file, verbose=verbose, ...) list(.createMassObject(mass=s$spectrum$mass, intensity=s$spectrum$intensity, metaData=s$metaData, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose)) } MALDIquantForeign/R/exportTab-methods.R0000644000175000017500000000251512523634201020731 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see setMethod(f=".exportTab", signature=signature(x="AbstractMassObject"), definition=function(x, file="", row.names=FALSE, col.names=FALSE, ...) { return(write.table(as.matrix(x), file=file, row.names=row.names, col.names=col.names, ... )) }) setMethod(f=".exportCsv", signature=signature(x="AbstractMassObject"), definition=function(x, file="", sep=",", row.names=FALSE, col.names=TRUE, ...) { return(.exportTab(x, file=file, sep=sep, row.names=row.names, col.names=col.names, ...)) }) MALDIquantForeign/R/export-methods.R0000644000175000017500000003605012553246651020316 0ustar sebastiansebastian## Copyright 2012-2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Export files #' #' This function provides a general interface to export #' \code{\link[MALDIquant]{AbstractMassObject-class}} objects (e.g. #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}}) #' into different file formats. #' #' @details #' Specific export functions: #' \tabular{ll}{ #' tab \tab \code{\link[MALDIquantForeign]{exportTab}} \cr #' csv \tab \code{\link[MALDIquantForeign]{exportCsv}} \cr #' imzML \tab \code{\link[MALDIquantForeign]{exportImzMl}} \cr #' msd \tab \code{\link[MALDIquantForeign]{exportMsd}} \cr #' mzML \tab \code{\link[MALDIquantForeign]{exportMzMl}} \cr #' } #' #' @usage #' \S4method{export}{AbstractMassObject}(x, file, type="auto", force=FALSE, \ldots) #' #' @param x a \code{\link[MALDIquant]{AbstractMassObject-class}} object or a #' \code{list} of \code{\link[MALDIquant]{AbstractMassObject-class}} objects. #' @param file \code{character}, file name. #' @param path \code{character}, path to directory in which the \code{list} of #' \code{\link[MALDIquant]{AbstractMassObject-class}} would be exported. #' @param type \code{character}, file format. If \code{type} is set to #' \dQuote{auto} the file extension is used. #' @param force \code{logical}, If \code{TRUE} the \code{file} would be #' overwritten or \code{path} would be created. #' @param \ldots arguments to be passed to specific export functions. #' #' @seealso #' \code{\link[MALDIquant]{MassPeaks-class}}, #' \code{\link[MALDIquant]{MassSpectrum-class}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' #' \dontrun{ #' library("MALDIquant") #' library("MALDIquantForeign") #' #' s <- list(createMassSpectrum(mass=1:5, intensity=1:5), #' createMassSpectrum(mass=1:5, intensity=1:5)) #' #' ## export a single spectrum #' export(s[[1]], file="spectrum.csv") #' ## identical to exportCsv(s[[1]], file="spectrum.csv") #' #' ## export a list of spectra #' export(s, path="spectra", type="csv") #' ## identical to exportCsv(s, path="spectra") #' } #' #' @aliases export export,AbstractMassObject-method export,list-method #' @rdname export-methods #' @docType methods #' @export setMethod(f="export", signature=signature(x="AbstractMassObject"), definition=function(x, file, type="auto", force=FALSE, ...) { return(.exportToFile(x=x, file=file, type=type, force=force, ...)) }) #' @usage #' \S4method{export}{list}(x, path, type, force=FALSE, \ldots) #' @rdname export-methods #' @export setMethod(f="export", signature=signature(x="list"), definition=function(x, path, type, force=FALSE, ...) { stopifnot(MALDIquant:::.isMassObjectList(x)) onefileSupport <- exportFormats$type[exportFormats$onefile] dots <- list(...) if (missing(path) && !is.null(dots$file)) { path <- dots$file dots$file <- NULL } isFile <- !isTRUE(file.info(path)$isdir) && tolower(.fileExtension(path)) %in% onefileSupport if (isFile) { do.call(.exportToFile, modifyList(list(x=x, file=path, type=type, force=force), dots)) } else { do.call(.exportToDir, modifyList(list(x=x, path=path, type=type, force=force), dots)) } }) #' Export to text files #' #' This function exports #' \code{\link[MALDIquant]{AbstractMassObject-class}} objects (e.g. #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}}) #' into different text file formats. #' #' @details #' \code{exportTab} and \code{exportCsv} use \code{\link[utils]{write.table}} #' with different defaults (\code{sep="\t"} in \code{exportTab} and #' \code{sep=","} in \code{exportCsv}). #' #' @usage #' \S4method{exportTab}{AbstractMassObject}(x, file, force=FALSE, \ldots) #' #' @param x a \code{\link[MALDIquant]{AbstractMassObject-class}} object or a #' \code{list} of \code{\link[MALDIquant]{AbstractMassObject-class}} objects. #' @param file \code{character}, file name. #' @param path \code{character}, path to directory in which the \code{list} of #' \code{\link[MALDIquant]{AbstractMassObject-class}} would be exported. #' @param force \code{logical}, If \code{TRUE} the \code{file} would be #' overwritten or \code{path} would be created. #' @param \ldots arguments to be passed to \code{\link[utils]{write.table}}. #' #' @seealso #' \code{\link[MALDIquant]{MassPeaks-class}}, #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[utils]{write.table}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' #' \dontrun{ #' library("MALDIquant") #' library("MALDIquantForeign") #' #' s <- list(createMassSpectrum(mass=1:5, intensity=1:5), #' createMassSpectrum(mass=1:5, intensity=1:5)) #' #' ## export a single spectrum #' exportTab(s[[1]], file="spectrum.tab") #' #' ## export a list of spectra and use ; as separator #' exportCsv(s, path="spectra", sep=";", force=TRUE) #' } #' #' @aliases exportTab exportTab,AbstractMassObject-method exportTab,list-method #' exportCsv exportCsv,AbstractMassObject-method exportCsv,list-method #' @rdname exportTab-methods #' @docType methods #' @export setMethod(f="exportTab", signature=signature(x="AbstractMassObject"), definition=function(x, file, force=FALSE, ...) { export(x, file=file, type="tab", force=force, ...) }) #' @usage #' \S4method{exportTab}{list}(x, path, force=FALSE, \ldots) #' @rdname exportTab-methods #' @export setMethod(f="exportTab", signature=signature(x="list"), definition=function(x, path, force=FALSE, ...) { export(x, path=path, type="tab", force=force, ...) }) #' @usage #' \S4method{exportCsv}{AbstractMassObject}(x, file, force=FALSE, \ldots) #' @rdname exportTab-methods #' @export setMethod(f="exportCsv", signature=signature(x="AbstractMassObject"), definition=function(x, file, force=FALSE, ...) { export(x, file=file, type="csv", force=force, ...) }) #' @usage #' \S4method{exportCsv}{list}(x, path, force=FALSE, \ldots) #' @rdname exportTab-methods #' @export setMethod(f="exportCsv", signature=signature(x="list"), definition=function(x, path, force=FALSE, ...) { export(x, path=path, type="csv", force=force, ...) }) #' Export to MSD files #' #' This function exports #' \code{\link[MALDIquant]{AbstractMassObject-class}} objects (e.g. #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}}) #' into mMass MSD files. #' #' @usage #' \S4method{exportMsd}{MassSpectrum}(x, file, force=FALSE, peaks, \ldots) #' #' @param x a \code{\link[MALDIquant]{MassSpectrum-class}} object or a #' \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} objects. #' @param file \code{character}, file name. #' @param path \code{character}, path to directory in which the \code{list} of #' \code{\link[MALDIquant]{AbstractMassObject-class}} would be exported. #' @param peaks a \code{\link[MALDIquant]{MassPeaks-class}} object or a #' \code{list} of \code{\link[MALDIquant]{MassPeaks-class}} objects. #' @param force \code{logical}, If \code{TRUE} the \code{file} would be #' overwritten or \code{path} would be created. #' @param \ldots arguments to be passed to \code{\link[utils]{write.table}}. #' #' @seealso #' \code{\link[MALDIquant]{MassPeaks-class}}, #' \code{\link[MALDIquant]{MassSpectrum-class}} #' #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/}, \cr #' mMass homepage: \url{http://mmass.org/} #' @examples #' #' \dontrun{ #' library("MALDIquant") #' library("MALDIquantForeign") #' #' s <- list(createMassSpectrum(mass=1:5, intensity=1:5), #' createMassSpectrum(mass=1:5, intensity=1:5)) #' p <- list(createMassPeaks(mass=4:5, intensity=4:5, snr=1:2), #' createMassPeaks(mass=4:5, intensity=4:5, snr=1:2)) #' #' ## export a single spectrum #' exportMsd(s[[1]], file="spectrum.msd") #' #' ## export a single spectrum with corresponding peaks #' exportMsd(s[[1]], file="spectrum.msd", peaks=p[[1]]) #' #' ## export a list of spectra with corresponding peaks #' exportMsd(s, path="spectra", peaks=p, force=TRUE) #' } #' #' @aliases exportMsd exportMsd,MassSpectrum-method exportMsd,list-method #' @rdname exportMsd-methods #' @docType methods #' @export setMethod(f="exportMsd", signature=signature(x="MassSpectrum"), definition=function(x, file, force=FALSE, peaks, ...) { if (!missing(peaks)) { stopifnot(isMassPeaks(peaks)) export(x, file=file, type="msd", force=force, peaks=peaks, ...) } else { export(x, file=file, type="msd", force=force, ...) } }) #' @usage #' \S4method{exportMsd}{list}(x, path, force=FALSE, peaks, \ldots) #' @rdname exportMsd-methods #' @export setMethod(f="exportMsd", signature=signature(x="list"), definition=function(x, path, force=FALSE, peaks, ...) { stopifnot(isMassSpectrumList(x)) if (!missing(peaks)) { stopifnot(isMassPeaksList(peaks)) export(x, path=path, type="msd", force=force, peaks=peaks, ...) } else { export(x, path=path, type="msd", force=force, ...) } }) #' Export to mzML files #' #' This function exports #' \code{\link[MALDIquant]{MassSpectrum-class}} objects into mzML files. #' #' @usage #' \S4method{exportMzMl}{MassSpectrum}(x, file, force=FALSE, \ldots) #' #' @param x a \code{\link[MALDIquant]{MassSpectrum-class}} object or a #' \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} objects. #' @param file \code{character}, file name. #' @param path \code{character}, path to directory in which the \code{list} of #' \code{\link[MALDIquant]{MassSpectrum-class}} would be exported. If #' \code{path} is a single filename all spectra will be exported to a single #' mzML file. #' @param force \code{logical}, If \code{TRUE} the \code{file} would be #' overwritten or \code{path} would be created. #' @param \ldots arguments to be passed to internal functions. #' #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}} #' #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/}, \cr #' HUPO Proteomics Standards Inititative mzML 1.1.0 Specification: #' \url{http://www.psidev.info/mzml_1_0_0} #' @examples #' #' \dontrun{ #' library("MALDIquant") #' library("MALDIquantForeign") #' #' s <- list(createMassSpectrum(mass=1:5, intensity=1:5), #' createMassSpectrum(mass=1:5, intensity=1:5)) #' #' ## export a single spectrum #' exportMzMl(s[[1]], file="spectrum.mzML") #' #' ## export a list of spectra #' exportMzMl(s, path="spectra.mzML") #' } #' #' @aliases exportMzMl exportMzMl,MassSpectrum-method exportMzMl,list-method #' @rdname exportMzMl-methods #' @docType methods #' @export setMethod(f="exportMzMl", signature=signature(x="MassSpectrum"), definition=function(x, file, force=FALSE, ...) { export(x, file=file, type="mzml", force=force, ...) }) #' @usage #' \S4method{exportMzMl}{list}(x, path, force=FALSE, \ldots) #' @rdname exportMzMl-methods #' @export setMethod(f="exportMzMl", signature=signature(x="list"), definition=function(x, path, force=FALSE, ...) { export(x, path=path, type="mzml", force=force, ...) }) #' Export to imzML files #' #' This function exports #' \code{\link[MALDIquant]{MassSpectrum-class}} objects into imzML files. #' #' @usage #' \S4method{exportImzMl}{MassSpectrum}(x, file, force=FALSE, processed=TRUE, #' coordinates=NULL, pixelSize=c(100, 100), \ldots) #' #' @param x a \code{\link[MALDIquant]{MassSpectrum-class}} object or a #' \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} objects. #' @param file \code{character}, file name. #' @param path \code{character}, path to directory in which the \code{list} of #' \code{\link[MALDIquant]{MassSpectrum-class}} would be exported. If #' \code{path} is a single filename all spectra will be exported to a single #' imzML file. #' @param force \code{logical}, If \code{TRUE} the \code{file} would be #' overwritten or \code{path} would be created. #' @param processed \code{logical}, If \code{TRUE} (default) the spectra will #' be saved in processed mode (means mass and intensity is stored for each #' spectra separately in contrast to continuous mode where the mass is stored #' only for one spectrum). #' @param coordinates \code{matrix}, 2 column matrix that contains the x- and #' y-coordinates for the spectra. #' @param pixelSize \code{numeric}, a vector of length 2 that contains the x and #' y pixel size in micrometers (default: \code{c(100, 100)}). #' @param \ldots arguments to be passed to internal functions. #' #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}} #' #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' #' Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, #' Laprevote O, Desbenoit N, Robbe M-F, Stoeckli M, Spengler B, Roempp A #' (2012)\cr #' imzML - A common data format for the flexible exchange and processing of mass #' spectrometry imaging data.\cr #' Journal of Proteomics 75 (16):5106-5110. \cr #' \url{http://dx.doi.org/10.1016/j.jprot.2012.07.026} #' @examples #' #' \dontrun{ #' library("MALDIquant") #' library("MALDIquantForeign") #' #' s <- list(createMassSpectrum(mass=1:5, intensity=1:5), #' createMassSpectrum(mass=1:5, intensity=1:5)) #' #' ## export a list of spectra #' exportImzMl(s, path="processed.imzML", coordinates=cbind(x=1:2, y=c(1, 1))) #' } #' #' @aliases exportImzMl exportImzMl,MassSpectrum-method exportImzMl,list-method #' @rdname exportImzMl-methods #' @docType methods #' @export setMethod(f="exportImzMl", signature=signature(x="MassSpectrum"), definition=function(x, file, force=FALSE, processed=TRUE, coordinates=NULL, pixelSize=c(100, 100), ...) { export(x, file=file, type="imzml", force=force, processed=processed, coordinates=coordinates, pixelSize=pixelSize, ...) }) #' @usage #' \S4method{exportImzMl}{list}(x, path, force=FALSE, processed=TRUE, #' coordinates=NULL, pixelSize=c(100, 100), \ldots) #' @rdname exportImzMl-methods #' @export setMethod(f="exportImzMl", signature=signature(x="list"), definition=function(x, path, force=FALSE, processed=TRUE, coordinates=NULL, pixelSize=c(100, 100), ...) { export(x, path=path, type="imzml", force=force, processed=processed, coordinates=coordinates, pixelSize=pixelSize, ...) }) MALDIquantForeign/R/uuid-functions.R0000644000175000017500000000407312523634201020275 0ustar sebastiansebastian## Copyright 2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see ## generate uuid needed for imzML idb files ## based on dplR::uuid.gen by Mikko Korpela ## should be compatible to: ## http://en.wikipedia.org/wiki/Universally_unique_identifier#Version_4_.28random.29 ## @param init used to create the md5 string, just for testing; don't change the ## default in other use cases. ## @return uuid string ## @noRd .uuid <- function(init=paste(c(Sys.info(), Sys.getpid(), unlist(R.version), Sys.getpid(), format(Sys.time(), "%Y%m%d%H%M%OS6 %Z"), runif(5L)), collapse = "")) { md5 <- digest::digest(init, algo="md5", serialize=FALSE) md5 <- strsplit(md5, "", fixed=TRUE)[[1L]] md5[13] <- "4" md5[17] <- c("8", "9", "a", "b")[strtoi(md5[17L], base=16L)%%4L + 1L] .paste0 <- function(...)paste0(..., collapse="") paste(.paste0(md5[1L:8L]), .paste0(md5[9L:12L]), .paste0(md5[13L:16L]), .paste0(md5[17L:20L]), .paste0(md5[21L:32L]), sep="-") } ## test uuid version 4 ## @param x character vector to test ## @return logical ## @noRd .isUuidV4 <- function(x) { grepl(paste0("^[0-9a-f]{8}-?", "[0-9a-f]{4}-?", "4[0-9a-f]{3}-?", "[89ab][0-9a-f]{3}-?", "[0-9a-f]{12}"), tolower(x)) } MALDIquantForeign/R/MALDIquantForeign-parallel.R0000644000175000017500000000543712601030514022323 0ustar sebastiansebastian## Copyright 2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Parallel Support in Package \pkg{MALDIquantForeign} #' #' \code{\link[MALDIquantForeign]{MALDIquantForeign-package}} offers multi-core #' support using \code{\link[parallel]{mclapply}} and #' \code{\link[parallel]{mcmapply}}. This approach is limited to unix-based #' platforms. #' #' Please note that not all import functions benfit from parallelisation. The #' current implementation is limited to run the parallelisation over different #' files. That's why only imports of multiple files could be run on multiple #' cores. E.g. a single mzML file containing 4 spectra would always be #' read on a single core. In contrast 4 mzML files each containing just one #' spectra could be read in using 4 cores. #' #' The improvement in the runtime depends on the amount of data to read, the #' proportion of parsing/decoding of the data, the amount of memory and the #' speed of the hard disk. #' #' Please note: It is possible that using parallelisation results in a worse #' runtime! #' #' @name MALDIquantForeign-parallel #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @keywords misc #' @seealso #' \code{\link[MALDIquant]{MALDIquant-parallel}}, #' \code{\link[parallel]{mclapply}}, #' \code{\link[parallel]{mcmapply}} #' #' @examples #' ## load packages #' library("MALDIquant") #' library("MALDIquantForeign") #' #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## run single-core import #' print(system.time( #' s1 <- importMzMl(exampleDirectory, centroided=TRUE, verbose=FALSE) #' )) #' #' if(.Platform$OS.type == "unix") { #' ## run multi-core import #' ## (because the example spectra are very small (just 5 data points) the #' ## multi-core solution is slower on most systems) #' print(system.time( #' s2 <- importMzMl(exampleDirectory, centroided=TRUE, mc.cores=2, #' verbose=FALSE) #' )) #' stopifnot(all.equal(s1, s2)) #' } #' @rdname MALDIquantForeign-parallel NULL MALDIquantForeign/R/download-function.R0000644000175000017500000000343112566326011020754 0ustar sebastiansebastian## Copyright 2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .isUrl <- function(x)grepl(pattern="^https?://|^ftp://", x=x) .download <- function(url, destfile, verbose=FALSE, ...) { if (missing(destfile)) { pattern <- paste0(.withoutFileExtension(basename(url)), "_") fileext <- paste0(".", .fileExtension(url)) tmpdir <- file.path(tempdir(), "MALDIquantForeign_download") if (!file.exists(tmpdir)) { dir.create(tmpdir, showWarnings=FALSE, recursive=TRUE) } destfile <- file.path(tmpdir, tempfile(pattern=pattern, tmpdir="", fileext=fileext)) } .msg(verbose, "Downloading ", paste0(url, collapse=", ") , " to ", paste0(destfile, collapse=", "), ".") for (i in seq(along=url)) { if (download.file(url=url[i], destfile=destfile[i], quiet=!verbose, mode="wb", ...)) { warning("Download of ", url[i], " failed!") } } destfile } .cleanupDownloadedTmpFiles <- function() { unlink(file.path(tempdir(), "MALDIquantForeign_download"), recursive=TRUE) } MALDIquantForeign/R/exportMzMl-methods.R0000644000175000017500000000227612523634201021106 0ustar sebastiansebastian## Copyright 2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see setMethod(f=".exportMzMl", signature=signature(x="MassSpectrum"), definition=function(x, file, id=.withoutFileExtension(basename(file)), ...) { return(.writeMzMlDocument(x=list(x), file=file, id=id, ...)) }) setMethod(f=".exportMzMl", signature=signature(x="list"), definition=function(x, file, id=.withoutFileExtension(basename(file)), ...) { return(.writeMzMlDocument(x=x, file=file, id=id, ...)) }) MALDIquantForeign/R/compression-functions.R0000644000175000017500000000635012523634201021670 0ustar sebastiansebastian## Copyright 2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .isCompressed <- function(x) { z <- c("bz2", "bzip2", "gz", "lzma", "xz") .fileExtension(x) %in% c("zip", z, paste("tar", z, sep=".")) } .isTar <- function(x)grepl(pattern="^tar", x=.fileExtension(x)) .isZip <- function(x)grepl(pattern="^zip$", x=.fileExtension(x)) .isPackedOrCompressed <- function(x) { .isCompressed(x) | .isTar(x) } # unpack/uncompress files and return temporary filenames .uncompress <- function(x, verbose=TRUE) { f <- lapply(x, function(path) { if (!.isPackedOrCompressed(path)) { return(x) } else { if (.isTar(path)) { return(.unpacking(x, fun=untar, verbose=verbose)) } else if (.isZip(path)) { return(.unpacking(x, fun=unzip, verbose=verbose)) } else { return(.gunzip(x, verbose=verbose)) } } }) unlist(f) } # unpack and return tmp filename .unpacking <- function(filename, destdir, fun, verbose=FALSE, ...) { if (missing(destdir)) { pattern <- paste0(.withoutFileExtension(basename(filename)), "_") destdir <- file.path(tempdir(), "MALDIquantForeign_uncompress", tempfile(pattern=pattern, tmpdir="")) } funName <- deparse(substitute(fun)) fun <- as.function(fun) .msg(verbose, funName, " ", filename, " to ", destdir, ".") unpacked <- fun(filename, exdir=destdir, ...) if (!length(unpacked)) { stop(funName, " failed!") } destdir } # gunzip and return tmp filename .gunzip <- function(filename, destfile, verbose=FALSE) { if (!file.exists(filename)) { stop(sQuote(filename), " doesn't exist!") } if (missing(destfile)) { tmpdir <- file.path(tempdir(), "MALDIquantForeign_uncompress") if (!file.exists(tmpdir)) { dir.create(tmpdir, showWarnings=FALSE, recursive=TRUE) } pattern <- paste0(.withoutFileExtension(basename(filename)), "_") fileext <- paste0(".", .fileExtension(.withoutCompressionExtension(filename))) destfile <- tempfile(pattern=pattern, tmpdir=tmpdir, fileext=fileext) } .msg(verbose, "gunzip ", filename, " to ", destfile, ".") fi <- gzfile(filename, open="rb") on.exit(close(fi)) fo <- file(destfile, open="wb") on.exit(close(fo), add=TRUE) repeat { b <- readBin(fi, what=raw(), n=1e6) ## n==1e6 => nearly 50Mb if (length(b)) { writeBin(b, con=fo) } else { break } } destfile } .cleanupUncompressedTmpFiles <- function() { unlink(file.path(tempdir(), "MALDIquantForeign_uncompress"), recursive=TRUE) } MALDIquantForeign/R/msd-functions.R0000644000175000017500000000732112523634201020111 0ustar sebastiansebastian## Copyright 2012-2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .writeMsdDocument <- function(x, file, peaks, encoding="utf-8") { ## stop if file isn't writeable if (file.exists(file) && file.access(file, 2) != 0) { stop("No permissions to write into ", sQuote(file), "!") } ## file handle f <- file(file, open="wt", encoding=encoding) ## header .writeXmlHeader(file=f, encoding=encoding) .writeXmlTag("mSD", attrs=c(version=2.2), close=FALSE, file=f) .writeMsdDescription(x, file=f) .writeMsdSpectrum(x, file=f) if (!missing(peaks)) { .writeMsdPeakList(peaks, file=f) } .writeCloseXmlTag("mSD", file=f) invisible(close(f)) } .writeMsdDescription <- function(x, file) { .writeXmlTag("description", intend=1, close=FALSE, file=file) .writeXmlTag("title", text=.createMsdTitle(file), intend=2, file=file) .writeXmlTag("date", attrs=c(value=.sanitize(metaData(x)$acquisitionDate)), intend=2, file=file) .writeXmlTag("operator", attrs=c(value=.sanitize(metaData(x)$owner)), intend=2, file=file) .writeXmlTag("contact", attrs=c(value=.sanitize(metaData(x)$owner)), intend=2, file=file) .writeXmlTag("institution", attrs=c(value=.sanitize(metaData(x)$institution)), intend=2, file=file) .writeXmlTag("instrument", attrs=c(value=.sanitize(metaData(x)$instrument)), intend=2, file=file) .writeXmlTag("notes", .sanitize(paste(metaData(x)$comments, collapse="\n")), intend=2, file=file) .writeCloseXmlTag("description", intend=1, file=file) } .writeMsdSpectrum <- function(x, file) { polarity <- paste(metaData(x)$ionizationMode, metaData(x)$polarity) if (length(polarity)) { polarity <- ifelse(grepl(pattern="+|positive", x=polarity), "1", "-1") } else { polarity <- "" } .writeXmlTag("spectrum", attrs=c(points=length(x), msLevel=ifelse(is.null(metaData(x)$msLevel), 1, metaData(x)$msLevel), polarity=polarity), close=FALSE, intend=1, file=file) .writeMsdArray(mass(x), name="mzArray", file=file) .writeMsdArray(intensity(x), name="intArray", file=file) .writeCloseXmlTag("spectrum", intend=1, file=file) } .writeMsdArray <- function(x, name, file) { .writeXmlTag(name, text=.base64encode(x, size=8, compressionType="gzip"), attrs=c(precision="64", compression="zlib", endian=.Platform$endian), intend=2, file=file) } .writeMsdPeakList <- function(x, file) { .writeXmlTag("peaklist", close=FALSE, intend=1, file=file) cat(paste0(" \n"), file=file, sep="", append=TRUE) .writeCloseXmlTag("peaklist", intend=1, file=file) } .createMsdTitle <- function(file) { .sanitize(.withoutFileExtension(basename(summary(file)$description))) } MALDIquantForeign/R/import-functions.R0000644000175000017500000004551012601030514020634 0ustar sebastiansebastian## Copyright 2012-2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Import files #' #' This function provides a general interface to import different file formats #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @details #' Specific import functions: #' \tabular{ll}{ #' txt \tab \code{\link[MALDIquantForeign]{importTxt}} \cr #' tab \tab \code{\link[MALDIquantForeign]{importTab}} \cr #' csv \tab \code{\link[MALDIquantForeign]{importCsv}} \cr #' fid \tab \code{\link[MALDIquantForeign]{importBrukerFlex}} \cr #' ciphergen \tab \code{\link[MALDIquantForeign]{importCiphergenXml}} \cr #' mzXML \tab \code{\link[MALDIquantForeign]{importMzXml}} \cr #' mzML \tab \code{\link[MALDIquantForeign]{importMzMl}} \cr #' imzML \tab \code{\link[MALDIquantForeign]{importImzMl}} \cr #' analyze \tab \code{\link[MALDIquantForeign]{importAnalyze}} \cr #' cdf \tab \code{\link[MALDIquantForeign]{importCdf}} \cr #' msd \tab \code{\link[MALDIquantForeign]{importMsd}} \cr #' } #' #' \code{path}: In addition to the above mentioned file types the #' following (compressed) archives are supported, too: #' zip, tar, tar.gz, tar.bz2, tar.xz. The archives are uncompressed in a #' temporary directory. Afterwards the \code{\link[MALDIquantForeign]{import}} #' function is called (with \code{type="auto"}). #' #' \code{pattern}: Sometimes unusual file extensions are used (e.g. #' \code{"*.xml"} for mzXML files). In this case a specific #' \code{pattern} could be defined to import files with an unusual file #' extension (e.g. \code{pattern="^.*\\.xml$"} to read all \code{*.xml} #' files in a directory; see \code{\link[base]{regexp}} for details). #' #' \code{excludePattern}: Sometimes some files should be excluded. E.g. #' to ignore additional aquired Bruker LIFT spectra #' (MALDI-TOF/TOF; which are not support, yet) you could use #' \code{excludePattern="([[:digit:]\\.]+)LIFT[\\\\/]1SRef"}. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param type \code{character}, file format. If \code{type} is set to #' \dQuote{auto} MALDIquant tries to detect the correct file type #' automatically. It often depends on the file extension #' (if \code{path} is a directory the most represented file extension is used; #' \code{pattern} argument is ignored). #' @param pattern \code{character}, a regular expression to find files in a #' directory (see details). #' @param excludePattern \code{character}, a regular expression to exclude #' files in a directory (see details). #' @param removeEmptySpectra \code{logical}, should empty spectra excluded? #' @param centroided \code{logical}, if \code{centroided=FALSE} (default) #' the data are treated as not centroided and a list of #' \code{\link[MALDIquant]{MassSpectrum-class}} objects is returned. Use #' \code{centroided=TRUE} to assume centroided data and get a list of #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' @param massRange \code{double}, limits of mass import (left/minimal mass, #' right/maximal mass). #' @param minIntensity \code{double}, minimal intensity to import. #' @param mc.cores number of cores to use (default 1; only unix-based platforms #' are supported, see #' \code{\link[MALDIquantForeign]{MALDIquantForeign-parallel}} for details). #' @param verbose \code{logical}, verbose output? #' @param \ldots arguments to be passed to specific import functions. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}} #' \code{\link[MALDIquantForeign]{MALDIquantForeign-parallel}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import mzXML files #' s <- import(exampleDirectory, type="mzXML") #' #' ## import tab delimited file with different file extension (default: *.tab) #' s <- import(exampleDirectory, type="tab", pattern="^.*\\.txt") #' #' ## import single mzML file #' s <- import(file.path(exampleDirectory, "tiny1.mzML1.1.mzML")) #' #' ## import gzipped csv file #' s <- import(file.path(exampleDirectory, "compressed", "csv1.csv.gz")) #' #' @rdname import-functions #' @export import <- function(path, type="auto", pattern, excludePattern=NULL, removeEmptySpectra=TRUE, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, mc.cores=1L, verbose=interactive(), ...) { ## download file if needed isUrl <- .isUrl(path) if (any(isUrl)) { path[isUrl] <- .download(path[isUrl], verbose=verbose) on.exit(.cleanupDownloadedTmpFiles()) } ## file exists? isReadable <- file.exists(path) & file.access(path, mode=4) == 0 if (any(!isReadable)) { stop(sQuote(path[!isReadable]), " doesn't exist or isn't readable!") } ## uncompress/unpack file if needed isCompressed <- .isPackedOrCompressed(path) if (any(isCompressed)) { path[isCompressed] <- .uncompress(path[isCompressed], verbose=verbose) on.exit(.cleanupUncompressedTmpFiles(), add=TRUE) } ## handle given file type i <- pmatch(tolower(type), c("auto", importFormats$type), nomatch=0, duplicates.ok=FALSE)-1 if (i == -1) { stop("File type ", sQuote(type), " is not supported!") } else if (i == 0) { ## auto detect file type if (!missing(pattern)) { warning("User defined ", sQuote("pattern"), " is ignored in auto-mode.") } return(.importAuto(path=path, excludePattern=excludePattern, removeEmptySpectra=removeEmptySpectra, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose, ...)) } else { ## user-defined file type if (missing(pattern)) { pattern <- importFormats$pattern[i] } handler <- get(importFormats$handler[i], mode="function") s <- unlist(MALDIquant:::.lapply(.files(path=path, pattern=pattern, excludePattern=excludePattern), handler, centroided=centroided, massRange=massRange, minIntensity=minIntensity, mc.cores=mc.cores, verbose=verbose, ...)) if (is.null(s)) { stop("Import failed! Unsupported file type?") } if (removeEmptySpectra) { emptyIdx <- MALDIquant::findEmptyMassObjects(s) if (length(emptyIdx)) { .msg(verbose, "Remove ", length(emptyIdx), " empty spectra.") return(s[-emptyIdx]) } } return(s) } } #' Import text files #' #' This function imports different text file formats #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' \code{importTab}, \code{importTxt} and \code{importCsv} use #' \code{\link[utils]{read.table}} with different defaults. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to \code{\link[utils]{read.table}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}}, #' \code{\link[utils]{read.table}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import txt files #' s <- importTxt(exampleDirectory) #' #' ## import csv files #' s <- importCsv(exampleDirectory) #' #' @rdname importTab-functions #' @export importTxt <- function(path, ...) { return(import(path=path, type="txt", ...)) } #' @rdname importTab-functions #' @export importTab <- function(path, ...) { return(import(path=path, type="tab", ...)) } #' @rdname importTab-functions #' @export importCsv <- function(path, ...) { return(import(path=path, type="csv", ...)) } #' Import Bruker Daltonics *flex files #' #' This function imports files in Bruker Daltonics *flex-series file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to #' \code{\link[readBrukerFlexData]{readBrukerFlexFile}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}}, #' \code{\link[readBrukerFlexData]{readBrukerFlexFile}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' s <- importBrukerFlex(exampleDirectory) #' #' @rdname importBrukerFlex-functions #' @export importBrukerFlex <- function(path, ...) { return(import(path=path, type="fid", ...)) } #' Import mzXML files #' #' This function imports files in mzXML file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to #' \code{\link[readMzXmlData]{readMzXmlFile}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}}, #' \code{\link[readMzXmlData]{readMzXmlFile}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/}, \cr #' Definition of \code{mzXML} format: #' \url{http://tools.proteomecenter.org/mzXMLschema.php} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import #' s <- importMzXml(exampleDirectory) #' #' @rdname importMzXml-functions #' @export importMzXml <- function(path, ...) { return(import(path=path, type="mzxml", ...)) } #' Import mzML files #' #' This function imports files in mzML file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to #' \code{\link[MALDIquantForeign]{import}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/}, \cr #' Definition of \code{mzML} format: #' \url{http://www.psidev.info/mzml_1_0_0\%20} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import #' s <- importMzMl(exampleDirectory) #' #' @rdname importMzMl-functions #' @export importMzMl <- function(path, ...) { return(import(path=path, type="mzml", ...)) } #' Import imzML files #' #' This function imports files in imzML file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param coordinates \code{matrix}, 2 column matrix that contains the x- and #' y-coordinates for spectra that should be imported. Other spectra would be #' ignored. #' @param \ldots arguments to be passed to #' \code{\link[MALDIquantForeign]{import}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/}, \cr #' Definition of \code{imzML} format: #' \url{http://www.imzml.org/} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import #' s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML")) #' #' ## import only spectra for pixel 1,1 and 2,1 #' s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML"), #' coordinates = cbind(1:2, c(1, 1))) #' #' @rdname importImzMl-functions #' @export importImzMl <- function(path, coordinates=NULL, ...) { return(import(path=path, type="imzml", coordinates=coordinates, ...)) } #' Import Ciphergen XML files #' #' This function imports files in Ciphergen XML file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to #' \code{\link[MALDIquantForeign]{import}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import #' s <- importCiphergenXml(exampleDirectory) #' #' @rdname importCiphergenXml-functions #' @export importCiphergenXml <- function(path, ...) { return(import(path=path, type="ciphergen", ...)) } #' Import Analyze 7.5 files #' #' This function imports files in Analyze 7.5 file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to #' \code{\link[MALDIquantForeign]{import}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} \cr #' \url{http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm}, #' \url{http://eeg.sourceforge.net/ANALYZE75.pdf} #' @rdname importAnalyze-functions #' @export importAnalyze <- function(path, ...) { return(import(path=path, type="analyze", ...)) } #' Import CDF files #' #' This function imports files in NetCDF file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects.\cr #' Please note that the \emph{RNetCDF} is needed. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to #' \code{\link[MALDIquantForeign]{import}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import #' if (requireNamespace("RNetCDF", quietly=TRUE)) { #' s <- importCdf(exampleDirectory) #' } else { #' message("You have to install the RNetCDF package to use importCdf.") #' } #' #' @rdname importCdf-functions #' @export importCdf <- function(path, ...) { return(import(path=path, type="cdf", ...)) } #' Import MSD files #' #' This function imports files in mMass MSD file format #' into \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects. #' #' @param path \code{character}, path to directory or file which should be read #' in. #' @param \ldots arguments to be passed to #' \code{\link[MALDIquantForeign]{import}}. #' #' @return a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or #' \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the #' \code{centroided} argument). #' @seealso #' \code{\link[MALDIquant]{MassSpectrum-class}}, #' \code{\link[MALDIquant]{MassPeaks-class}} #' @author Sebastian Gibb #' @references \url{http://strimmerlab.org/software/maldiquant/}, \cr #' mMass homepage: \url{http://mmass.org/} #' @examples #' #' library("MALDIquant") #' library("MALDIquantForeign") #' #' ## get example directory #' exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") #' #' ## import #' s <- importMsd(exampleDirectory) #' #' @rdname importMsd-functions #' @export importMsd <- function(path, ...) { return(import(path=path, type="msd", ...)) } MALDIquantForeign/R/ibd-functions.R0000644000175000017500000000434412523634201020066 0ustar sebastiansebastian## Copyright 2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .writeIbd <- function(x, filename, uuid, processed=TRUE) { ibd <- file(filename, open="wb") on.exit(close(ibd)) uuid <- gsub("-", "", tolower(uuid)) uuid <- substring(uuid, seq(1L, 32L, by=2L), seq(2L, 32L, by=2L)) uuid <- strtoi(uuid, base=16L) writeBin(uuid, con=ibd, size=1L, endian="little") for (i in seq(along=x)) { if (processed || i == 1L) { writeBin(as.double(x[[i]]@mass), con=ibd, size=8L, endian="little") } writeBin(as.double(x[[i]]@intensity), con=ibd, size=8L, endian="little") } } .ibdOffsets <- function(x, processed=TRUE, encodedLengthSize=8L) { ## start at 16 (16 bytes for UUID) n <- rep(unlist(lapply(x, length)), each=2L) encodedLength <- n * encodedLengthSize if (processed) { offsets <- cumsum(c(16L, encodedLength[-length(n)])) } else { sel <- seq(from=2L, to=length(n), by=2L) offsets <- rep.int(16L, length(n)) offsets[sel] <- 16L + cumsum(encodedLength[sel]) } matrix(c(offsets, n, encodedLength), nrow=length(n), dimnames=list(rep(c("mass", "intensity"), times=length(x)), c("offset", "length", "encodedLength"))) } .addIbdOffsets <- function(x, processed=TRUE, encodedLengthSize=8L) { offsets <- .ibdOffsets(x, processed=processed, encodedLengthSize=encodedLengthSize) i <- split(1:nrow(offsets), rep(1:length(x), each=2L)) for (j in seq(along=x)) { x[[j]]@metaData$imaging$offsets <- offsets[i[[j]],] } x } MALDIquantForeign/R/importCdf-functions.R0000644000175000017500000000535012601026330021250 0ustar sebastiansebastian## Copyright 2013-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' @author Pietro Franceschi \email{pietro.franceschi@@fmach.it}, Sebastian Gibb #' \email{mail@@sebastiangibb.de} #' @keywords internal #' @noRd ## original code written by Pietro Franceschi ## modified for MALDIquantForeign by Sebastian Gibb .importCdf <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE) { if (!requireNamespace("RNetCDF", quietly=TRUE)) { stop("For netCDF support the ", sQuote("RNetCDF"), " package is needed. \n", "Please install ", sQuote("RNetCDF"), ": install.packages(\"RNetCDF}\")") } nc <- RNetCDF::open.nc(file) on.exit(RNetCDF::close.nc(nc)) scanIndex <- as.integer(RNetCDF::var.get.nc(nc, variable="scan_index")) scanLength <- as.integer(RNetCDF::var.get.nc(nc, variable="point_count")) retentionTime <- as.double(RNetCDF::var.get.nc(nc, variable="scan_acquisition_time")) ## read and process the spectra/peaks l <- vector(mode="list", length=length(scanIndex)) for (i in seq(along=l)) { mass <- as.double(RNetCDF::var.get.nc(nc, variable="mass_values", start=scanIndex[i]+1L, count=scanLength[i])) intensity <- as.double(RNetCDF::var.get.nc(nc, variable="intensity_values", start=scanIndex[i]+1L, count=scanLength[i])) l[[i]] <- .createMassObject(mass=mass, intensity=intensity, metaData=list(file=file, number=i, retentionTime=retentionTime[i], scanIndex=scanIndex[i]), centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose) } l } MALDIquantForeign/R/importCiphergenXml-functions.R0000644000175000017500000000260612601026330023142 0ustar sebastiansebastian## Copyright 2013-2014 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importCiphergenXml <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, verbose=FALSE) { .msg(verbose, "Reading spectrum from ", sQuote(file), " ...") if (!file.exists(file)) { stop("File ", sQuote(file), " doesn't exists!") } ## read file s <- .parseCiphergenXml(file=file) list(.createMassObject(mass=s$spectrum$mass, intensity=s$spectrum$intensity, metaData=s$metaData, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose)) } MALDIquantForeign/R/msg-functions.R0000644000175000017500000000154612523634201020117 0ustar sebastiansebastian## Copyright 2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .msg <- function(verbose, ...) { if (verbose) { message(...) } } MALDIquantForeign/R/imzMl-functions.R0000644000175000017500000000422512523634201020416 0ustar sebastiansebastian## Copyright 2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .writeImzMlDocument <- function(x, file, id=.withoutFileExtension(basename(file)), processed=TRUE, uuid=.uuid(), coordinates=NULL, pixelSize=c(100, 100), ...) { if(isMassSpectrum(x)) { x <- list(x) } if (is.null(metaData(x[[1L]])$imaging) && is.null(coordinates)) { stop("The spectra contain no imaging information.") } isCoordinatesMatrix <- is.matrix(coordinates) && ncol(coordinates) == 2L && nrow(coordinates) == length(x) if (!is.null(coordinates) && !isCoordinatesMatrix) { stop("The ", sQuote("coordinates"), " argument has to be a matrix with two columns (x and y position)!") } if (isCoordinatesMatrix) { size <- apply(coordinates, 2, max) dimension <- size * pixelSize x[[1L]]@metaData$imaging <- list(size=size, dim=dimension, pixelSize=pixelSize) coordinates(x) <- coordinates } ibdFile <- .changeFileExtension(file, "ibd") .writeIbd(x, ibdFile, uuid=uuid, processed=processed) sha1 <- digest::digest(ibdFile, algo="sha1", file=TRUE) .writeMzMlDocument(x=.addIbdOffsets(x), file=file, id=id, imsArgs=list(uuid=uuid, sha1=sha1, processed=processed), ...) } MALDIquantForeign/R/parseCiphergenXml.R0000644000175000017500000000545112615212670020746 0ustar sebastiansebastian## Copyright 2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Parse Ciphergen XML files. #' #' This function parses Ciphergen XML files. #' #' @param file \code{character}, path to Ciphergen XML file #' @param verbose \code{logical}, verbose output? #' #' @return Returns a list with metadata and spectra. #' #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @keywords internal #' @noRd .parseCiphergenXml <- function(file, ...) { ## metaData listNames <- c("name", "ionSourceVoltage", "digitizerRate", "massCalibrationA", "massCalibrationB", "massCalibrationT0", "massCalibrationInfo", "spotCorrectionFactor") xpath <- paste0("//spectrum/", c("spectrumName", paste0("acquisitionInfo/setting/", listNames[2:3]), paste0("processingParameters/massCalibration/", listNames[-c(1:3)])), "/text()") doc <- xmlParse(file, ...) metaData <- XML::xpathApply(doc=doc, path=xpath, fun=XML::xmlValue) names(metaData) <- listNames metaData[listNames[-c(1, 7)]] <- lapply(metaData[-c(1, 7)], as.double) metaData$file <- normalizePath(file) intensity <- XML::xpathSApply(doc=doc, path="//spectrum/tofData/tofDataSamples/text()", fun=XML::xmlValue) intensity <- as.double(strsplit(intensity, "[[:space:]]+")[[1]]) intensity <- intensity[!is.na(intensity)] ## tof2mass ## mass = U*(A*(tof-t0)^2 + B) ## Calibration formula was taken from: ## http://bioinformatics.mdanderson.org/Supplements/Datasets/KuererQC/scripts.zip ## file: ciphergenXMLreader.pl n <- 0:(length(intensity)-1) time <- metaData$spotCorrectionFactor*n/metaData$digitizerRate tof <- time-metaData$massCalibrationT0 mass <- metaData$ionSourceVoltage * (sign(tof) * metaData$massCalibrationA * tof*tof + metaData$massCalibrationB) list(spectrum=list(mass=mass, intensity=intensity), metaData=metaData) } MALDIquantForeign/R/exportImzMl-methods.R0000644000175000017500000000244012553245455021264 0ustar sebastiansebastian## Copyright 2013 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see setMethod(f=".exportImzMl", signature=signature(x="MassSpectrum"), definition=function(x, file, id=.withoutFileExtension(basename(file)), processed=TRUE, ...) { .writeImzMlDocument(x=x, file=file, id=id, processed=processed, ...) }) setMethod(f=".exportImzMl", signature=signature(x="list"), definition=function(x, file, id=.withoutFileExtension(basename(file)), processed=TRUE, ...) { .writeImzMlDocument(x=x, file=file, id=id, processed=processed, ...) }) MALDIquantForeign/R/filename-functions.R0000644000175000017500000000576312523634201021116 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .cleanFilename <- function(x) { gsub(pattern="([[:punct:]]|[[:space:]])+", replacement="_", x=x) } #' Determine file extension #' #' @param x \code{character}, filename. #' #' @return \code{character}, file extension. #' #' @seealso \code{\link[MALDIquant]{MassSpectrum-class}} #' @keywords internal #' @noRd #' @examples #' library("MALDIquantForeign") #' files <- c("/home/foo/bar.txt", "foobar.pdf") #' MALDIquantForeign:::.fileExtension(files) #' .fileExtension <- function(x) { pos <- regexpr(pattern="(\\.tar)?\\.([[:alnum:]]+)$|(/|\\\\)+[^.\\\\/]+$", text=x) ifelse(pos > -1L, substring(x, pos+1L), x) } .withoutFileExtension <- function(x) { sub(pattern="\\.[[:alnum:]]+?$|(/|\\\\)+[^.\\\\/]+$", replacement="", x=.withoutCompressionExtension(x)) } .withoutCompressionExtension <- function(x) { sub(pattern="\\.(zip|gz|bz2|bzip2|xz|lzma)+$", replacement="", x=x) } .changeFileExtension <- function(x, newExtension) { paste(.withoutFileExtension(x), newExtension, sep=".") } .cutFilenames <- function(x) { l <- strsplit(x, split=.Platform$file.sep, fixed=TRUE) nCol <- unlist(lapply(l, length)) mCol <- max(nCol) m <- matrix(NA, nrow=length(x), ncol=mCol) for (i in seq(along=l)) { cols <- 1:nCol[i] m[i, cols] <- l[[i]] } isIdentical <- apply(m, 2, function(co)all(co[1] == co)) isIdentical[is.na(isIdentical)] <- FALSE m <- as.matrix(m[, !isIdentical]) if (length(m)) { filenames <- apply(m, 1, function(r) { do.call(file.path, as.list(na.omit(r))) }) } else { filenames <- basename(x) } filenames } .uniqueBaseFilenames <- function(x, fileExtension="csv", sep="_") { filenames <- .cutFilenames(.withoutFileExtension(x)) filenames <- .cleanFilename(filenames) empty <- nchar(filenames) <= 0 filenames[empty] <- seq_along(empty) filenames <- .make.unique(filenames, sep=sep) paste(filenames, fileExtension, sep=".") } ## let make unique start by 1 .make.unique <- function(x, sep="_") { tmp <- lapply(split(x, x), function(y) { n <- length(y) if (n > 1) { fmt <- paste0("%s%s%0", floor(log10(n))+1, "d") y <- sprintf(fmt=fmt, y, sep, 1:n) } return(y) }) unsplit(tmp, x) } MALDIquantForeign/R/base64encode-functions.R0000644000175000017500000000372112523634201021570 0ustar sebastiansebastian## Copyright 2012 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see #' Converts double to base64 character. #' #' This function converts a \code{double} vector to a base64 encoded #' \code{character} vector. #' #' @param x \code{double}, vector #' @param size \code{integer}, number of bytes per element in the byte stream #' (see \code{size} in \code{\link[base]{writeBin}}). #' @param endian \code{character}, the endian-ness #' (see \code{endian} in \code{\link[base]{writeBin}}). #' @param compressionType \code{character}, type of compression to use for #' compression of \code{x} (see \code{type} in #' \code{\link[base]{memCompress}}. #' @return Vector of type \code{character}. #' @rdname base64-encode #' @author Sebastian Gibb \email{mail@@sebastiangibb.de} #' @seealso \code{\link[base64enc]{base64encode}} from \pkg{base64enc} package #' @keywords internal #' .base64encode <- function(x, size, endian=.Platform$endian, compressionType=c("none", "gzip")) { x <- writeBin(as.double(x), con=raw(), size=size, endian=endian) compressionType <- match.arg(compressionType, choices=c("none", "gzip"), several.ok=FALSE) x <- memCompress(from=x, type=compressionType) base64enc::base64encode(x) } MALDIquantForeign/R/importImzMl-functions.R0000644000175000017500000001036512601026330021606 0ustar sebastiansebastian## Copyright 2013-2015 Sebastian Gibb ## ## ## This file is part of MALDIquantForeign for R and related languages. ## ## MALDIquantForeign is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by ## the Free Software Foundation, either version 3 of the License, or ## (at your option) any later version. ## ## MALDIquantForeign is distributed in the hope that it will be useful, ## but WITHOUT ANY WARRANTY; without even the implied warranty of ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ## GNU General Public License for more details. ## ## You should have received a copy of the GNU General Public License ## along with MALDIquantForeign. If not, see .importImzMl <- function(file, centroided=FALSE, massRange=c(0, Inf), minIntensity=0, coordinates=NULL, verbose=FALSE) { .msg(verbose, "Reading spectrum from ", sQuote(file), " ...") if (!file.exists(file)) { stop("File ", sQuote(file), " doesn't exists!") } ibdFilename <- .changeFileExtension(file, "ibd") if (!file.exists(ibdFilename)) { stop("File ", sQuote(ibdFilename), " doesn't exists!") } s <- .parseMzMl(file=file, verbose=verbose) ibd <- file(ibdFilename, open="rb") on.exit(close(ibd)) ## test UUID uuid <- paste0(readBin(ibd, raw(), n=16, size=1, signed=TRUE, endian= "little"), collapse="") if (is.null(s$ims$uuid)) { warning("There is not any UUID in ", sQuote(file), "!") } else if (tolower(uuid) != tolower(s$ims$uuid)) { warning("The UUID in ", sQuote(file) , " and ", sQuote(ibdFilename), "do not match!") } else if (!.isUuidV4(uuid)) { warning("The UUID: ", uuid, " is not valid!") } ## test checksums if (!is.null(s$ims$md5)) { .testChecksum(ibdFilename, s$ims$md5, algo="md5", verbose=verbose) } else if (!is.null(s$ims$sha1)) { .testChecksum(ibdFilename, s$ims$sha1, algo="sha1", verbose=verbose) } else { warning("At least one checksum (SHA-1 or MD5) for the idb file ", "should be provided in the imzML file.") } sel <- seq_along(s$ims$ibd) isCoordinatesMatrix <- is.matrix(coordinates) && ncol(coordinates) == 2L if (!is.null(coordinates) && !isCoordinatesMatrix) { stop("The ", sQuote("coordinates"), " argument has to be a matrix with two columns (x and y position)!") } if (isCoordinatesMatrix) { pos <- do.call(rbind, lapply(s$spectra, function(x)x$metaData$imaging$pos)) sel <- match(paste(coordinates[, 1L], coordinates[, 2L], sep=":"), paste(pos[, 1L], pos[, 2L], sep=":")) if (anyNA(sel)) { warning("The following rows contain invalid coordinates: ", paste(which(is.na(sel)), collapse=", ")) sel <- sort(sel[!is.na(sel)]) } } .readValues <- function(file, x, column, isSeekNeeded) { if (isSeekNeeded) { ## WARNING: we know that `seek` is discouraged on some platforms, ## namely Windows. See `?seek` for details. seek(file, where=x[column, "offset"]) } n <- x[column, "length"] e <- x[column, "encodedLength"] return(readBin(file, double(), n=n, size=e/n, signed=TRUE, endian="little")) } n <- length(sel) spectra <- vector(mode="list", length=n) isProcessed <- s$ims$type == "processed" isSeekNeeded <- length(s$ims$ibd) > length(sel) if (!isProcessed) { mass <- .readValues(ibd, s$ims$ibd[[sel[1L]]], "mass", isSeekNeeded) } ## read mass and intensity values for (i in seq(along=sel)) { .msg(verbose, "Reading binary data for spectrum ", i, "/", n, " ...") m <- modifyList(s$metaData, s$spectra[[sel[i]]]$metaData) m$file <- file if (isProcessed) { mass <- .readValues(ibd, s$ims$ibd[[sel[i]]], "mass", isSeekNeeded) } intensity <- .readValues(ibd, s$ims$ibd[[sel[i]]], "intensity", isSeekNeeded) spectra[[i]] <- .createMassObject(mass=mass, intensity=intensity, metaData=m, centroided=centroided, massRange=massRange, minIntensity=minIntensity, verbose=verbose) } spectra } MALDIquantForeign/inst/0000755000175000017500000000000012615440602015750 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/0000755000175000017500000000000012576343313020244 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/tiny_continuous.ibd0000644000175000017500000000021012522426621024161 0ustar sebastiansebastian4VxLޯ4Vx?@@@@@@ @"@$@$@"@ @@@MALDIquantForeign/inst/exampledata/tiny1-centroided.mzXML3.0.mzXML0000644000175000017500000000316612325512134025603 0ustar sebastiansebastian P/AAAAAAAABAGAAAAAAAAEAAAAAAAAAAQBwAAAAAAABACAAAAAAAAEAgAAAAAAAAQBAAAAAAAABAIgAAAAAAAEAUAAAAAAAAQCQAAAAAAAA= 0 0 1cf2b3695447d2dd698b465e27f452a80192dd62 MALDIquantForeign/inst/exampledata/tiny1.mzXML3.0.mzXML0000644000175000017500000000313412325512134023460 0ustar sebastiansebastian P/AAAAAAAABAGAAAAAAAAEAAAAAAAAAAQBwAAAAAAABACAAAAAAAAEAgAAAAAAAAQBAAAAAAAABAIgAAAAAAAEAUAAAAAAAAQCQAAAAAAAA= 0 0 b87b09a4f34561d5572f9a6d30056106f819bc69 MALDIquantForeign/inst/exampledata/tiny_processed.ibd0000644000175000017500000000026012522426621023747 0ustar sebastiansebastian4VxLޯ4Vx?@@@@@@ @"@$@@@ @"@$@$@"@ @@@MALDIquantForeign/inst/exampledata/tiny_processed.imzML0000644000175000017500000001235412522426621024250 0ustar sebastiansebastian MALDIquantForeign/inst/exampledata/csv1.csv0000644000175000017500000000005012325512134021617 0ustar sebastiansebastian"mass","intensity" 1,6 2,7 3,8 4,9 5,10 MALDIquantForeign/inst/exampledata/tiny1.mzML1.1.mzML0000644000175000017500000000673012325512134023204 0ustar sebastiansebastian AAAAAAAA8D8AAAAAAAAAQAAAAAAAAAhAAAAAAAAAEEAAAAAAAAAUQA== AADAQAAA4EAAAABBAAAQQQAAIEE= AAAAAAAA8D8AAAAAAAAAQAAAAAAAAAhAAAAAAAAAEEAAAAAAAAAUQA== AAAAAAAAJEAAAAAAAAAiQAAAAAAAACBAAAAAAAAAHEAAAAAAAAAYQA== MALDIquantForeign/inst/exampledata/compressed/0000755000175000017500000000000012615440505022403 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/compressed/csv1.csv.gz0000644000175000017500000000007412325512134024410 0ustar sebastiansebastianSM,.VQ+I+,T21212ֱ2ѱ214v(MALDIquantForeign/inst/exampledata/compressed/csv.zip0000644000175000017500000000031612325512134023716 0ustar sebastiansebastianPK bXBv((csv1.csvUT )Q)Qux "mass","intensity" 1,6 2,7 3,8 4,9 5,10 PK bXBv((csv1.csvUT)Qux PKNjMALDIquantForeign/inst/exampledata/compressed/csv.tar.gz0000644000175000017500000000023512522426621024325 0ustar sebastiansebastianα 0y9HMS}X:d t"| ߤ&] *pOuGu/ߴ~RO-ܶǤ%߷jKjh:7Mp38=n(MALDIquantForeign/inst/exampledata/ascii.txt0000644000175000017500000000002512325512134022061 0ustar sebastiansebastian1 6 2 7 3 8 4 9 5 10 MALDIquantForeign/inst/exampledata/ciphergen/0000755000175000017500000000000012325512134022177 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/ciphergen/tiny.xml0000644000175000017500000000153512325512134023710 0ustar sebastiansebastian tiny example 20000 2.5e+008 Quadratic 24000000 0.0013 0 20000 hand made 1 false 1 2 3 4 5 MALDIquantForeign/inst/exampledata/tiny1-compressed.mzML1.1.mzML0000644000175000017500000000665412325512134025353 0ustar sebastiansebastian eJxjYACBD/YMEOAAoTigtACUFnEAADZ/Alw= eJxjYDjgwMDwAIgZHBkYBIBYwREAJcMDFA== eJxjYACBD/YMEOAAoTigtACUFnEAADZ/Alw= eJxjYAABFQcwxaAEpRWgtAyUlnAAACEsAds= MALDIquantForeign/inst/exampledata/tiny1-centroided.mzML1.1.mzML0000644000175000017500000000753212325512134025323 0ustar sebastiansebastian AAAAAAAA8D8AAAAAAAAAQAAAAAAAAAhAAAAAAAAAEEAAAAAAAAAUQA== AADAQAAA4EAAAABBAAAQQQAAIEE= AADAQAAA4EAAAABBAAAQQQAAIEE= AAAAAAAA8D8AAAAAAAAAQAAAAAAAAAhAAAAAAAAAEEAAAAAAAAAUQA== AAAAAAAAJEAAAAAAAAAiQAAAAAAAACBAAAAAAAAAHEAAAAAAAAAYQA== MALDIquantForeign/inst/exampledata/brukerflex/0000755000175000017500000000000012325512134022404 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/brukerflex/0_A1/0000755000175000017500000000000012325512134023064 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/brukerflex/0_A1/1/0000755000175000017500000000000012325512134023224 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/brukerflex/0_A1/1/1SLin/0000755000175000017500000000000012325512134024152 5ustar sebastiansebastianMALDIquantForeign/inst/exampledata/brukerflex/0_A1/1/1SLin/acqu0000644000175000017500000000071112325512134025025 0ustar sebastiansebastian##.SPECTROMETER TYPE= TOF ##.IONIZATION MODE= LD+ ##$AQOP_m= 0 ##$BYTORDA= 0 ##$CMT1= TESTSAMPLE1 ##$CMT2= TESTSAMPLE2 ##$CMT3= TESTSAMPLE3 ##$CMT4= TESTSAMPLE4 ##$DELAY= 10000 ##$DW= 20 ##$HPClBHi= 0 ##$HPClBLo= 0 ##$HPClOrd= 0 ##$HPClUse= no ##$Lift1= 0 ##$Lift2= 0 ##$ML1= 2400000 ##$ML1_raw= 2400000 ##$ML2= 280 ##$ML2_raw= 280 ##$ML3= -0.0013 ##$ML3_raw= -0.0013 ##$NoSHOTS= 100 ##$SPType= 0 ##$TD= 5 ##$TLift= 0 MALDIquantForeign/inst/exampledata/brukerflex/0_A1/1/1SLin/fid0000644000175000017500000000002412325512134024633 0ustar sebastiansebastianMALDIquantForeign/inst/exampledata/tiny_continuous.imzML0000644000175000017500000001235412522426621024467 0ustar sebastiansebastian MALDIquantForeign/inst/exampledata/csv2.csv0000644000175000017500000000002512325512134021622 0ustar sebastiansebastian1;6 2;7 3;8 4;9 5;10 MALDIquantForeign/inst/exampledata/tiny1.msd0000644000175000017500000000106712522450613022012 0ustar sebastiansebastian tiny eJxjYACBD/YMEOAAoTigtACUFnEAADZ/Alw= eJxjYDjgwMDwAIgZHBkYBIBYwREAJcMDFA== MALDIquantForeign/inst/exampledata/tiny.cdf0000644000175000017500000000071412325512134021676 0ustar sebastiansebastianCDF  scan_number point_number  scan_index4 point_count<scan_acquisition_timeD mass_valuesTintensity_values\?@? @ @ @@@@@ @"@$MALDIquantForeign/inst/exampledata/tiny1-compressed.mzXML3.0.mzXML0000644000175000017500000000304412325512134025622 0ustar sebastiansebastian eJyz/8AABg4SUJoBSstAaQ4orQClBaC0EpQWgdIqEBoA0joENg== 0 0 7e7ef0ea030f6a56d34a4ebd446e22b22844d432 MALDIquantForeign/inst/doc/0000755000175000017500000000000012615440602016515 5ustar sebastiansebastianMALDIquantForeign/inst/doc/MALDIquantForeign-intro.R0000644000175000017500000000552512615440602023211 0ustar sebastiansebastian## ----setup, include=FALSE, cache=FALSE----------------------------------- library("knitr") opts_chunk$set(tidy.opts=list(width.cutoff=45), tidy=FALSE, fig.align="center", fig.height=4.25, comment=NA, prompt=TRUE) ## ----env, echo=FALSE----------------------------------------------------- suppressPackageStartupMessages(library("MALDIquant")) suppressPackageStartupMessages(library("MALDIquantForeign")) ## ----fileformats--------------------------------------------------------- supportedFileFormats() ## ----mqsetup, eval=FALSE------------------------------------------------- # install.packages(c("MALDIquant", "MALDIquantForeign")) ## ----mqlibrary, eval=FALSE----------------------------------------------- # library("MALDIquant") # library("MALDIquantForeign") ## ----import-------------------------------------------------------------- ## get the example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") spectra <- import(file.path(exampleDirectory, "brukerflex"), verbose=FALSE) spectra[[1]] ## ----importbrukerflex---------------------------------------------------- spectra <- importBrukerFlex(file.path(exampleDirectory, "brukerflex"), verbose=FALSE) spectra[[1]] ## ----importcsvcompressed------------------------------------------------- spectra <- importCsv(file.path(exampleDirectory, "compressed", "csv.tar.gz"), verbose=FALSE) spectra[[1]] spectra <- importCsv(file.path(exampleDirectory, "compressed", "csv.zip"), verbose=FALSE) spectra[[1]] ## ----importremote, eval=FALSE-------------------------------------------- # spectra <- import(paste0("http://www.meb.ki.se/", # "~yudpaw/papers/spikein_xml.zip"), # centroided=FALSE, verbose=TRUE) ## ----centroided---------------------------------------------------------- peaks <- import(file.path(exampleDirectory, "ascii.txt"), centroided=TRUE, verbose=FALSE) peaks ## ----masspectrum--------------------------------------------------------- spectra <- list( createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=6:10)) ## ----export1------------------------------------------------------------- export(spectra[[1]], file="spectrum1.csv") import("spectrum1.csv") ## ----exportpath, eval=TRUE----------------------------------------------- export(spectra, type="csv", path="spectra", force=TRUE) list.files("spectra") ## ----mqvignette, eval=FALSE---------------------------------------------- # vignette(topic="MALDIquant", package="MALDIquant") ## ----sessioninfo, echo=FALSE, results="asis"----------------------------- toLatex(sessionInfo(), locale=FALSE) MALDIquantForeign/inst/doc/MALDIquantForeign-intro.pdf0000644000175000017500000042236212615440602023563 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Ě񓝔Tp(V_XC"Ǧ_̴@JN-T)8WZH{Ϙfu `+=Fh$HE/"˱6$[K'-6Y TP@݁$vi*_ݻ|;ㅩ6&p"XV:c"p_&b n0"A~j nlh슔]i5U24&YdwYۯw+}bx 6ZC4ܡ RT旉TzDI?3h>^ι) 'WN j9^|T=sLiu8$”]%Ze!EŪPRbW`mZ"1FoRh·{Ark1ceLT/ s&!3$NQ-\/l(v7.B 1p˾n!H(US?j*U[~鴬[}<BěӔhjЃqhFqSVi팒~HNк~=5j H5M8sr,oLe&Oull?Ұ#JOR 좄`&H#@T:$Xq J!i(ņs Qa$9S]ΗΦJE (qY%ւ"MZ8ɢ:fMMh~̆TY: 04nY`)LBM2cQꊔ o~EKugs:U0>}>VPx1<Z׼֋>'6~_BG1NjJd"w~=s@?'efԫLu[فdXN yv ^_A~5z gFGx+xc!.Ghmj!Ǥ&Oקt|n؂~-]/ D/h :k Gl<}tc_EIȤwơᆟp/{ie[D3>Ăb2I"7;UHcy6$: y7B0NS㾼xEbNԖ=&vPXSڲTN߂.Sᑎ=Ӿ&Q>e4<\h(":¸D;f|+N->`&x}^Sm"W~2dt㸖Z#dq X`$K܎XJ;EmC1ݔzAUmv3©/1*zH8>"04D[ <‘GԒHLCesdT\g+Y>Htkф\X%G 7P@^L.ڗDCy%l+F,lmmBN@^X )lD[˔YM̦uy,:W^5n [^E@g~#x2ʧcH+y}#ցIlG!\ji[x9J{ r5݌ :0ww;ytSzL_3IqФPe dאpvLE΍'BңgrnɗNgՈSX!?(Q"nl&bW7ߢt.}Yz)F}@"989IHĶo_XmLL)na^F'D$옏"_4"ȭWD |z\[[gjVfOhJ<^#g@8G}c佮;FD(|pF*o=vzr7ʨ l6_;u=:WÀJ=DJΎ gi3̀1_2|ڊD_n;RTyaQÝT םm=oA u30*{[q+$W_*w avDm7DآZWد~Ыz/ɺJ6,_}d s♪L0MBtOd(G™C7>VqY^5K<<:oxW3--/>z'? ,P=)| Xͅ/>,#r&J:\9l:dyumZW1/`Q[[+[wɈH% )RO(Vt R|ʤThcptr gjœ ~oU& PֱM1bׂ `X4y+ցd۷G5/MB$bQ,U0JkI8FGӃDq%_r2 j-z~o@{$u ¡vITkQGð^qBnTuxb⨿ƶY)wx#Su~y䒶+f=31$‹I nJrn[ζ]6?wPjbӜî*AYy{Ծ0rXGf('lDQ#xG9d\F~mq(<\.f`/R_o"#l^*m={'riaBp:7lU)xB_sOe#a>nZ"2>rfI|w\K0>H_-s}>LHFjyASaq&lH]KG%&:z 'uq֋c$u9z:rl0Hzߠ y LEVNq"5sy.H92G!ڎ\H<ǝKv&,QQAe'H;oM{ ?LDQfյ#Ju*[G u'9Z_ ]O--A i9wHmbل[[!a?[Rɜn.Qۮ)=h O2f}hB 5YGjmI*T Hhw-:1lO^4A>-?|" endstream endobj 115 0 obj << /Length1 1452 /Length2 6614 /Length3 0 /Length 7603 /Filter /FlateDecode >> stream xڍT?tstt7H c`lFHw ! wv~^uss_Xu x`e8 (j@ /(bABx,`7 QD-8  E$E%@(&xdh00EqpDrvȻ @vA _!إHW >>OOO^/A A:d oix,CGnqP(w ` q5p~;ۀ@pW7@eM^`E"(E @Y^`o}E@juJ0;E D B7:0V2]``G9(ߘ O`/#߯ ]aT pW= ?ExH7w{[(lg `Dɏד%Javp-SV3P{^_q/w]c#*r̂$7k,HgH:kk&\>pBȇWMbgGwŒԬukgv'cI6:R(Ұw`6t$:(E˫[I֯?з?K{7ΖZyyDn;"1Z-onQ\꧌42l;mq`p\Rh#j^#1sqJ@Vq_LGmf`h xPY]sMQ*Gg=tK-5t|>s`e+]OLuD{;knY<}Ռa&R|Do;!TWHF`Zkbp͝گNxqvi^?C)h?9v 5i= @"@]ߑ r1p(%p'~e?v?KkwA9TĹtPi_iYARQ38èv?S& ˱?,Cr~(&7z(Frljf-v$2ADrMqxy'bE16uѣ%g/A6dRV'  &z+&bf=rģ&"nw&zikݒWеB/M /STqf x]1D  j hUytŎ5_14i%I-Ũ^ gcr4*֒=ݕ]Mt  'ˏ_W!N+N:L4R+f+ i#NmN= U!(LyM~rb7|܊S|5w9{6j7So,A b50ѧl!ԛw4"u,1$|r/•^,tFI$|kqtn{l5ؒT шhf [[`4hCxZq0?^Jn'|nf'/|. 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If you use it, please support the project by citing it in publications: \begin{quote} \bibentry{MALDIquant} \end{quote} If you have any questions, bugs, or suggestions do not hesitate to contact me (\email{mail@sebastiangibb.de}). \\ Please visit \url{http://strimmerlab.org/software/maldiquant/}. \section{Introduction} \Mq{} should be device and platform independent. That's why it has not any import/export functions. \\ \MqF{} fills this gap and provides import/export routines for various file formats: <>= supportedFileFormats() @ \section{Setup} After starting \R{} we could install \Mq{} and \MqF{} directly from \CRAN{} using \Rfunction{install.packages}: <>= install.packages(c("MALDIquant", "MALDIquantForeign")) @ Before we can use \Mq{} and \MqF{} we have to load the packages. <>= library("MALDIquant") library("MALDIquantForeign") @ \section{Import} \MqF{} provides an \Rfunction{import} function that tries to auto-detect the correct file type. Because this would never be perfect \MqF{} offers also many \Rfunction{import*} functions like \Rfunction{importBrukerFlex}, \Rfunction{importMzMl}, etc. Please see the manual page of \Rfunction{import} for a complete list (\Rfunction{?import}).\\ First we try to import some example data in Bruker Daltonics *flex-series file format using the \Rfunction{import} function. <>= ## get the example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") spectra <- import(file.path(exampleDirectory, "brukerflex"), verbose=FALSE) spectra[[1]] @ Next we use the \Rfunction{importBrukerFlex} function (the result is the same as above). <>= spectra <- importBrukerFlex(file.path(exampleDirectory, "brukerflex"), verbose=FALSE) spectra[[1]] @ \MqF{} supports compressed files, too (\emph{zip}, \emph{tar.\{bz2, gz,xz\}}). <>= spectra <- importCsv(file.path(exampleDirectory, "compressed", "csv.tar.gz"), verbose=FALSE) spectra[[1]] spectra <- importCsv(file.path(exampleDirectory, "compressed", "csv.zip"), verbose=FALSE) spectra[[1]] @ Remote files are supported as well. Data are taken from \citet{Tan2006}. <>= spectra <- import(paste0("http://www.meb.ki.se/", "~yudpaw/papers/spikein_xml.zip"), centroided=FALSE, verbose=TRUE) @ If you want to read peak lists (centroided data) instead of spectra data you have to set \Rfunction{centroided=TRUE}. <>= peaks <- import(file.path(exampleDirectory, "ascii.txt"), centroided=TRUE, verbose=FALSE) peaks @ \section{Export} The export routines in \MqF{} are very similar to the import routines. Please see manual page of \Rfunction{export} for a complete list of supported export routines (\Rfunction{?export}). First we create a simple list of \Robject{MassSpectrum} objects using \Rfunction{createMassSpectrum}. <>= spectra <- list( createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=6:10)) @ Now we want to export the first spectrum into a CSV file. <>= export(spectra[[1]], file="spectrum1.csv") import("spectrum1.csv") @ Exporting every file by hand is cumbersome. We want to export the whole list of spectra. Instead of \Robject{file} we use \Robject{path} now to specify a directory. Please note that we have to add the file type/format information now (we can use the \Robject{type} argument or the corresponding \Rfunction{export*} function). If the path doesn't exists we will get an error. To force \Rfunction{export} to create/overwrite the given path, we set the argument \Robject{force=TRUE}. <>= export(spectra, type="csv", path="spectra", force=TRUE) list.files("spectra") @ \section{Analyse Mass Spectrometry Data} Please have a look at the corresponding vignette shipped with \Mq{} and the \Mq{} website: \url{http://strimmerlab.org/software/maldiquant/}. <>= vignette(topic="MALDIquant", package="MALDIquant") @ \section{Session Information} <>= toLatex(sessionInfo(), locale=FALSE) @ \bibliographystyle{apalike} \bibliography{bibliography} \end{document} MALDIquantForeign/man/0000755000175000017500000000000012601030514015536 5ustar sebastiansebastianMALDIquantForeign/man/MALDIquantForeign-package.Rd0000644000175000017500000000117112615213711022636 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/package.R \docType{package} \name{MALDIquantForeign-package} \alias{MALDIquantForeign-package} \title{Import/Export routines for MALDIquant} \description{ This package reads and writes different file formats of mass spectrometry data into/from MALDIquant objects. } \details{ \tabular{ll}{ Package: \tab MALDIquantForeign \cr License: \tab GPL (>= 3)\cr URL: \tab http://strimmerlab.org/software/maldiquant/\cr } } \author{ Sebastian Gibb \email{mail@sebastiangibb.de} } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \keyword{package} MALDIquantForeign/man/importCiphergenXml-functions.Rd0000644000175000017500000000221612615213711023663 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importCiphergenXml} \alias{importCiphergenXml} \title{Import Ciphergen XML files} \usage{ importCiphergenXml(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[MALDIquantForeign]{import}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in Ciphergen XML file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import s <- importCiphergenXml(exampleDirectory) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}} } MALDIquantForeign/man/exportImzMl-methods.Rd0000644000175000017500000000474112615213711021775 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/export-methods.R \docType{methods} \name{exportImzMl,MassSpectrum-method} \alias{exportImzMl} \alias{exportImzMl,MassSpectrum-method} \alias{exportImzMl,list-method} \title{Export to imzML files} \usage{ \S4method{exportImzMl}{MassSpectrum}(x, file, force=FALSE, processed=TRUE, coordinates=NULL, pixelSize=c(100, 100), \ldots) \S4method{exportImzMl}{list}(x, path, force=FALSE, processed=TRUE, coordinates=NULL, pixelSize=c(100, 100), \ldots) } \arguments{ \item{x}{a \code{\link[MALDIquant]{MassSpectrum-class}} object or a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} objects.} \item{file}{\code{character}, file name.} \item{force}{\code{logical}, If \code{TRUE} the \code{file} would be overwritten or \code{path} would be created.} \item{processed}{\code{logical}, If \code{TRUE} (default) the spectra will be saved in processed mode (means mass and intensity is stored for each spectra separately in contrast to continuous mode where the mass is stored only for one spectrum).} \item{coordinates}{\code{matrix}, 2 column matrix that contains the x- and y-coordinates for the spectra.} \item{pixelSize}{\code{numeric}, a vector of length 2 that contains the x and y pixel size in micrometers (default: \code{c(100, 100)}).} \item{path}{\code{character}, path to directory in which the \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} would be exported. If \code{path} is a single filename all spectra will be exported to a single imzML file.} \item{\ldots}{arguments to be passed to internal functions.} } \description{ This function exports \code{\link[MALDIquant]{MassSpectrum-class}} objects into imzML files. } \examples{ \dontrun{ library("MALDIquant") library("MALDIquantForeign") s <- list(createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=1:5)) ## export a list of spectra exportImzMl(s, path="processed.imzML", coordinates=cbind(x=1:2, y=c(1, 1))) } } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, Laprevote O, Desbenoit N, Robbe M-F, Stoeckli M, Spengler B, Roempp A (2012)\cr imzML - A common data format for the flexible exchange and processing of mass spectrometry imaging data.\cr Journal of Proteomics 75 (16):5106-5110. \cr \url{http://dx.doi.org/10.1016/j.jprot.2012.07.026} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}} } MALDIquantForeign/man/exportTab-methods.Rd0000644000175000017500000000421112615213711021443 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/export-methods.R \docType{methods} \name{exportTab,AbstractMassObject-method} \alias{exportCsv} \alias{exportCsv,AbstractMassObject-method} \alias{exportCsv,list-method} \alias{exportTab} \alias{exportTab,AbstractMassObject-method} \alias{exportTab,list-method} \title{Export to text files} \usage{ \S4method{exportTab}{AbstractMassObject}(x, file, force=FALSE, \ldots) \S4method{exportTab}{list}(x, path, force=FALSE, \ldots) \S4method{exportCsv}{AbstractMassObject}(x, file, force=FALSE, \ldots) \S4method{exportCsv}{list}(x, path, force=FALSE, \ldots) } \arguments{ \item{x}{a \code{\link[MALDIquant]{AbstractMassObject-class}} object or a \code{list} of \code{\link[MALDIquant]{AbstractMassObject-class}} objects.} \item{file}{\code{character}, file name.} \item{force}{\code{logical}, If \code{TRUE} the \code{file} would be overwritten or \code{path} would be created.} \item{path}{\code{character}, path to directory in which the \code{list} of \code{\link[MALDIquant]{AbstractMassObject-class}} would be exported.} \item{\ldots}{arguments to be passed to \code{\link[utils]{write.table}}.} } \description{ This function exports \code{\link[MALDIquant]{AbstractMassObject-class}} objects (e.g. \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}}) into different text file formats. } \details{ \code{exportTab} and \code{exportCsv} use \code{\link[utils]{write.table}} with different defaults (\code{sep="\t"} in \code{exportTab} and \code{sep=","} in \code{exportCsv}). } \examples{ \dontrun{ library("MALDIquant") library("MALDIquantForeign") s <- list(createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=1:5)) ## export a single spectrum exportTab(s[[1]], file="spectrum.tab") ## export a list of spectra and use ; as separator exportCsv(s, path="spectra", sep=";", force=TRUE) } } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MassPeaks-class}}, \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[utils]{write.table}} } MALDIquantForeign/man/exportMsd-methods.Rd0000644000175000017500000000411412615213711021462 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/export-methods.R \docType{methods} \name{exportMsd,MassSpectrum-method} \alias{exportMsd} \alias{exportMsd,MassSpectrum-method} \alias{exportMsd,list-method} \title{Export to MSD files} \usage{ \S4method{exportMsd}{MassSpectrum}(x, file, force=FALSE, peaks, \ldots) \S4method{exportMsd}{list}(x, path, force=FALSE, peaks, \ldots) } \arguments{ \item{x}{a \code{\link[MALDIquant]{MassSpectrum-class}} object or a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} objects.} \item{file}{\code{character}, file name.} \item{force}{\code{logical}, If \code{TRUE} the \code{file} would be overwritten or \code{path} would be created.} \item{peaks}{a \code{\link[MALDIquant]{MassPeaks-class}} object or a \code{list} of \code{\link[MALDIquant]{MassPeaks-class}} objects.} \item{path}{\code{character}, path to directory in which the \code{list} of \code{\link[MALDIquant]{AbstractMassObject-class}} would be exported.} \item{\ldots}{arguments to be passed to \code{\link[utils]{write.table}}.} } \description{ This function exports \code{\link[MALDIquant]{AbstractMassObject-class}} objects (e.g. \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}}) into mMass MSD files. } \examples{ \dontrun{ library("MALDIquant") library("MALDIquantForeign") s <- list(createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=1:5)) p <- list(createMassPeaks(mass=4:5, intensity=4:5, snr=1:2), createMassPeaks(mass=4:5, intensity=4:5, snr=1:2)) ## export a single spectrum exportMsd(s[[1]], file="spectrum.msd") ## export a single spectrum with corresponding peaks exportMsd(s[[1]], file="spectrum.msd", peaks=p[[1]]) ## export a list of spectra with corresponding peaks exportMsd(s, path="spectra", peaks=p, force=TRUE) } } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/}, \cr mMass homepage: \url{http://mmass.org/} } \seealso{ \code{\link[MALDIquant]{MassPeaks-class}}, \code{\link[MALDIquant]{MassSpectrum-class}} } MALDIquantForeign/man/supportedFileFormats-functions.Rd0000644000175000017500000000335112615213711024225 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/fileFormats.R \name{supportedFileFormats} \alias{supportedFileFormats} \title{Supported file formats} \usage{ supportedFileFormats() } \value{ a \code{list} with two named elements (\code{import} and \code{export}) containing a \code{character} vector of supported file types. } \description{ This function prints all file formats supported by \code{\link{MALDIquantForeign-package}}. } \details{ \subsection{Import}{ \tabular{ll}{ txt \tab \code{\link[MALDIquantForeign]{importTxt}} \cr tab \tab \code{\link[MALDIquantForeign]{importTab}} \cr csv \tab \code{\link[MALDIquantForeign]{importCsv}} \cr fid \tab \code{\link[MALDIquantForeign]{importBrukerFlex}} \cr ciphergen \tab \code{\link[MALDIquantForeign]{importCiphergenXml}} \cr mzXML \tab \code{\link[MALDIquantForeign]{importMzXml}} \cr mzML \tab \code{\link[MALDIquantForeign]{importMzMl}} \cr imzML \tab \code{\link[MALDIquantForeign]{importImzMl}} \cr analyze \tab \code{\link[MALDIquantForeign]{importAnalyze}} \cr cdf \tab \code{\link[MALDIquantForeign]{importCdf}} \cr msd \tab \code{\link[MALDIquantForeign]{importMsd}} \cr } } \subsection{Export}{ \tabular{ll}{ tab \tab \code{\link[MALDIquantForeign]{exportTab}} \cr csv \tab \code{\link[MALDIquantForeign]{exportCsv}} \cr imzML \tab \code{\link[MALDIquantForeign]{exportImzMl}} \cr msd \tab \code{\link[MALDIquantForeign]{exportMsd}} \cr mzML \tab \code{\link[MALDIquantForeign]{exportMzMl}} \cr } } } \examples{ library("MALDIquantForeign") supportedFileFormats() } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquantForeign]{export}}, \code{\link[MALDIquantForeign]{import}} } MALDIquantForeign/man/MALDIquantForeign-parallel.Rd0000644000175000017500000000377612615213711023054 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/MALDIquantForeign-parallel.R \name{MALDIquantForeign-parallel} \alias{MALDIquantForeign-parallel} \title{Parallel Support in Package \pkg{MALDIquantForeign}} \description{ \code{\link[MALDIquantForeign]{MALDIquantForeign-package}} offers multi-core support using \code{\link[parallel]{mclapply}} and \code{\link[parallel]{mcmapply}}. This approach is limited to unix-based platforms. } \details{ Please note that not all import functions benfit from parallelisation. The current implementation is limited to run the parallelisation over different files. That's why only imports of multiple files could be run on multiple cores. E.g. a single mzML file containing 4 spectra would always be read on a single core. In contrast 4 mzML files each containing just one spectra could be read in using 4 cores. The improvement in the runtime depends on the amount of data to read, the proportion of parsing/decoding of the data, the amount of memory and the speed of the hard disk. Please note: It is possible that using parallelisation results in a worse runtime! } \examples{ ## load packages library("MALDIquant") library("MALDIquantForeign") exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## run single-core import print(system.time( s1 <- importMzMl(exampleDirectory, centroided=TRUE, verbose=FALSE) )) if(.Platform$OS.type == "unix") { ## run multi-core import ## (because the example spectra are very small (just 5 data points) the ## multi-core solution is slower on most systems) print(system.time( s2 <- importMzMl(exampleDirectory, centroided=TRUE, mc.cores=2, verbose=FALSE) )) stopifnot(all.equal(s1, s2)) } } \author{ Sebastian Gibb \email{mail@sebastiangibb.de} } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MALDIquant-parallel}}, \code{\link[parallel]{mclapply}}, \code{\link[parallel]{mcmapply}} } \keyword{misc} MALDIquantForeign/man/export-methods.Rd0000644000175000017500000000434012615213711021017 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/export-methods.R \docType{methods} \name{export,AbstractMassObject-method} \alias{export} \alias{export,AbstractMassObject-method} \alias{export,list-method} \title{Export files} \usage{ \S4method{export}{AbstractMassObject}(x, file, type="auto", force=FALSE, \ldots) \S4method{export}{list}(x, path, type, force=FALSE, \ldots) } \arguments{ \item{x}{a \code{\link[MALDIquant]{AbstractMassObject-class}} object or a \code{list} of \code{\link[MALDIquant]{AbstractMassObject-class}} objects.} \item{file}{\code{character}, file name.} \item{type}{\code{character}, file format. If \code{type} is set to \dQuote{auto} the file extension is used.} \item{force}{\code{logical}, If \code{TRUE} the \code{file} would be overwritten or \code{path} would be created.} \item{path}{\code{character}, path to directory in which the \code{list} of \code{\link[MALDIquant]{AbstractMassObject-class}} would be exported.} \item{\ldots}{arguments to be passed to specific export functions.} } \description{ This function provides a general interface to export \code{\link[MALDIquant]{AbstractMassObject-class}} objects (e.g. \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}}) into different file formats. } \details{ Specific export functions: \tabular{ll}{ tab \tab \code{\link[MALDIquantForeign]{exportTab}} \cr csv \tab \code{\link[MALDIquantForeign]{exportCsv}} \cr imzML \tab \code{\link[MALDIquantForeign]{exportImzMl}} \cr msd \tab \code{\link[MALDIquantForeign]{exportMsd}} \cr mzML \tab \code{\link[MALDIquantForeign]{exportMzMl}} \cr } } \examples{ \dontrun{ library("MALDIquant") library("MALDIquantForeign") s <- list(createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=1:5)) ## export a single spectrum export(s[[1]], file="spectrum.csv") ## identical to exportCsv(s[[1]], file="spectrum.csv") ## export a list of spectra export(s, path="spectra", type="csv") ## identical to exportCsv(s, path="spectra") } } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MassPeaks-class}}, \code{\link[MALDIquant]{MassSpectrum-class}} } MALDIquantForeign/man/base64-encode.Rd0000644000175000017500000000177712615213711020367 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/base64encode-functions.R \name{.base64encode} \alias{.base64encode} \title{Converts double to base64 character.} \usage{ .base64encode(x, size, endian = .Platform$endian, compressionType = c("none", "gzip")) } \arguments{ \item{x}{\code{double}, vector} \item{size}{\code{integer}, number of bytes per element in the byte stream (see \code{size} in \code{\link[base]{writeBin}}).} \item{endian}{\code{character}, the endian-ness (see \code{endian} in \code{\link[base]{writeBin}}).} \item{compressionType}{\code{character}, type of compression to use for compression of \code{x} (see \code{type} in \code{\link[base]{memCompress}}.} } \value{ Vector of type \code{character}. } \description{ This function converts a \code{double} vector to a base64 encoded \code{character} vector. } \author{ Sebastian Gibb \email{mail@sebastiangibb.de} } \seealso{ \code{\link[base64enc]{base64encode}} from \pkg{base64enc} package } \keyword{internal} MALDIquantForeign/man/importTab-functions.Rd0000644000175000017500000000260412615213711022005 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importTxt} \alias{importCsv} \alias{importTab} \alias{importTxt} \title{Import text files} \usage{ importTxt(path, ...) importTab(path, ...) importCsv(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[utils]{read.table}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports different text file formats into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \details{ \code{importTab}, \code{importTxt} and \code{importCsv} use \code{\link[utils]{read.table}} with different defaults. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import txt files s <- importTxt(exampleDirectory) ## import csv files s <- importCsv(exampleDirectory) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}}, \code{\link[utils]{read.table}} } MALDIquantForeign/man/importImzMl-functions.Rd0000644000175000017500000000304712615213711022331 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importImzMl} \alias{importImzMl} \title{Import imzML files} \usage{ importImzMl(path, coordinates = NULL, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{coordinates}{\code{matrix}, 2 column matrix that contains the x- and y-coordinates for spectra that should be imported. Other spectra would be ignored.} \item{\ldots}{arguments to be passed to \code{\link[MALDIquantForeign]{import}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in imzML file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML")) ## import only spectra for pixel 1,1 and 2,1 s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML"), coordinates = cbind(1:2, c(1, 1))) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/}, \cr Definition of \code{imzML} format: \url{http://www.imzml.org/} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}} } MALDIquantForeign/man/importAnalyze-functions.Rd0000644000175000017500000000202612615213711022700 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importAnalyze} \alias{importAnalyze} \title{Import Analyze 7.5 files} \usage{ importAnalyze(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[MALDIquantForeign]{import}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in Analyze 7.5 file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} \cr \url{http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm}, \url{http://eeg.sourceforge.net/ANALYZE75.pdf} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}} } MALDIquantForeign/man/importMsd-functions.Rd0000644000175000017500000000221112615213711022014 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importMsd} \alias{importMsd} \title{Import MSD files} \usage{ importMsd(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[MALDIquantForeign]{import}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in mMass MSD file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import s <- importMsd(exampleDirectory) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/}, \cr mMass homepage: \url{http://mmass.org/} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}} } MALDIquantForeign/man/importCdf-functions.Rd0000644000175000017500000000242012615213711021767 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importCdf} \alias{importCdf} \title{Import CDF files} \usage{ importCdf(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[MALDIquantForeign]{import}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in NetCDF file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects.\cr Please note that the \emph{RNetCDF} is needed. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import if (requireNamespace("RNetCDF", quietly=TRUE)) { s <- importCdf(exampleDirectory) } else { message("You have to install the RNetCDF package to use importCdf.") } } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}} } MALDIquantForeign/man/exportMzMl-methods.Rd0000644000175000017500000000324012615213711021615 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/export-methods.R \docType{methods} \name{exportMzMl,MassSpectrum-method} \alias{exportMzMl} \alias{exportMzMl,MassSpectrum-method} \alias{exportMzMl,list-method} \title{Export to mzML files} \usage{ \S4method{exportMzMl}{MassSpectrum}(x, file, force=FALSE, \ldots) \S4method{exportMzMl}{list}(x, path, force=FALSE, \ldots) } \arguments{ \item{x}{a \code{\link[MALDIquant]{MassSpectrum-class}} object or a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} objects.} \item{file}{\code{character}, file name.} \item{force}{\code{logical}, If \code{TRUE} the \code{file} would be overwritten or \code{path} would be created.} \item{path}{\code{character}, path to directory in which the \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} would be exported. If \code{path} is a single filename all spectra will be exported to a single mzML file.} \item{\ldots}{arguments to be passed to internal functions.} } \description{ This function exports \code{\link[MALDIquant]{MassSpectrum-class}} objects into mzML files. } \examples{ \dontrun{ library("MALDIquant") library("MALDIquantForeign") s <- list(createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=1:5)) ## export a single spectrum exportMzMl(s[[1]], file="spectrum.mzML") ## export a list of spectra exportMzMl(s, path="spectra.mzML") } } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/}, \cr HUPO Proteomics Standards Inititative mzML 1.1.0 Specification: \url{http://www.psidev.info/mzml_1_0_0} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}} } MALDIquantForeign/man/importBrukerFlex-functions.Rd0000644000175000017500000000233012615213711023344 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importBrukerFlex} \alias{importBrukerFlex} \title{Import Bruker Daltonics *flex files} \usage{ importBrukerFlex(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[readBrukerFlexData]{readBrukerFlexFile}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in Bruker Daltonics *flex-series file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") s <- importBrukerFlex(exampleDirectory) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}}, \code{\link[readBrukerFlexData]{readBrukerFlexFile}} } MALDIquantForeign/man/importMzXml-functions.Rd0000644000175000017500000000235712615213711022353 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importMzXml} \alias{importMzXml} \title{Import mzXML files} \usage{ importMzXml(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[readMzXmlData]{readMzXmlFile}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in mzXML file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import s <- importMzXml(exampleDirectory) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/}, \cr Definition of \code{mzXML} format: \url{http://tools.proteomecenter.org/mzXMLschema.php} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}}, \code{\link[readMzXmlData]{readMzXmlFile}} } MALDIquantForeign/man/import-functions.Rd0000644000175000017500000001075212615213711021361 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{import} \alias{import} \title{Import files} \usage{ import(path, type = "auto", pattern, excludePattern = NULL, removeEmptySpectra = TRUE, centroided = FALSE, massRange = c(0, Inf), minIntensity = 0, mc.cores = 1L, verbose = interactive(), ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{type}{\code{character}, file format. If \code{type} is set to \dQuote{auto} MALDIquant tries to detect the correct file type automatically. It often depends on the file extension (if \code{path} is a directory the most represented file extension is used; \code{pattern} argument is ignored).} \item{pattern}{\code{character}, a regular expression to find files in a directory (see details).} \item{excludePattern}{\code{character}, a regular expression to exclude files in a directory (see details).} \item{removeEmptySpectra}{\code{logical}, should empty spectra excluded?} \item{centroided}{\code{logical}, if \code{centroided=FALSE} (default) the data are treated as not centroided and a list of \code{\link[MALDIquant]{MassSpectrum-class}} objects is returned. Use \code{centroided=TRUE} to assume centroided data and get a list of \code{\link[MALDIquant]{MassPeaks-class}} objects.} \item{massRange}{\code{double}, limits of mass import (left/minimal mass, right/maximal mass).} \item{minIntensity}{\code{double}, minimal intensity to import.} \item{mc.cores}{number of cores to use (default 1; only unix-based platforms are supported, see \code{\link[MALDIquantForeign]{MALDIquantForeign-parallel}} for details).} \item{verbose}{\code{logical}, verbose output?} \item{\ldots}{arguments to be passed to specific import functions.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function provides a general interface to import different file formats into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \details{ Specific import functions: \tabular{ll}{ txt \tab \code{\link[MALDIquantForeign]{importTxt}} \cr tab \tab \code{\link[MALDIquantForeign]{importTab}} \cr csv \tab \code{\link[MALDIquantForeign]{importCsv}} \cr fid \tab \code{\link[MALDIquantForeign]{importBrukerFlex}} \cr ciphergen \tab \code{\link[MALDIquantForeign]{importCiphergenXml}} \cr mzXML \tab \code{\link[MALDIquantForeign]{importMzXml}} \cr mzML \tab \code{\link[MALDIquantForeign]{importMzMl}} \cr imzML \tab \code{\link[MALDIquantForeign]{importImzMl}} \cr analyze \tab \code{\link[MALDIquantForeign]{importAnalyze}} \cr cdf \tab \code{\link[MALDIquantForeign]{importCdf}} \cr msd \tab \code{\link[MALDIquantForeign]{importMsd}} \cr } \code{path}: In addition to the above mentioned file types the following (compressed) archives are supported, too: zip, tar, tar.gz, tar.bz2, tar.xz. The archives are uncompressed in a temporary directory. Afterwards the \code{\link[MALDIquantForeign]{import}} function is called (with \code{type="auto"}). \code{pattern}: Sometimes unusual file extensions are used (e.g. \code{"*.xml"} for mzXML files). In this case a specific \code{pattern} could be defined to import files with an unusual file extension (e.g. \code{pattern="^.*\\.xml$"} to read all \code{*.xml} files in a directory; see \code{\link[base]{regexp}} for details). \code{excludePattern}: Sometimes some files should be excluded. E.g. to ignore additional aquired Bruker LIFT spectra (MALDI-TOF/TOF; which are not support, yet) you could use \code{excludePattern="([[:digit:]\\.]+)LIFT[\\\\/]1SRef"}. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import mzXML files s <- import(exampleDirectory, type="mzXML") ## import tab delimited file with different file extension (default: *.tab) s <- import(exampleDirectory, type="tab", pattern="^.*\\\\.txt") ## import single mzML file s <- import(file.path(exampleDirectory, "tiny1.mzML1.1.mzML")) ## import gzipped csv file s <- import(file.path(exampleDirectory, "compressed", "csv1.csv.gz")) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}} \code{\link[MALDIquantForeign]{MALDIquantForeign-parallel}} } MALDIquantForeign/man/importMzMl-functions.Rd0000644000175000017500000000225712615213711022162 0ustar sebastiansebastian% Generated by roxygen2: do not edit by hand % Please edit documentation in R/import-functions.R \name{importMzMl} \alias{importMzMl} \title{Import mzML files} \usage{ importMzMl(path, ...) } \arguments{ \item{path}{\code{character}, path to directory or file which should be read in.} \item{\ldots}{arguments to be passed to \code{\link[MALDIquantForeign]{import}}.} } \value{ a \code{list} of \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects (depending on the \code{centroided} argument). } \description{ This function imports files in mzML file format into \code{\link[MALDIquant]{MassSpectrum-class}} or \code{\link[MALDIquant]{MassPeaks-class}} objects. } \examples{ library("MALDIquant") library("MALDIquantForeign") ## get example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") ## import s <- importMzMl(exampleDirectory) } \author{ Sebastian Gibb } \references{ \url{http://strimmerlab.org/software/maldiquant/}, \cr Definition of \code{mzML} format: \url{http://www.psidev.info/mzml_1_0_0\%20} } \seealso{ \code{\link[MALDIquant]{MassSpectrum-class}}, \code{\link[MALDIquant]{MassPeaks-class}} } MALDIquantForeign/vignettes/0000755000175000017500000000000012615440602017003 5ustar sebastiansebastianMALDIquantForeign/vignettes/bibliography.bib0000644000175000017500000000250212330410473022130 0ustar sebastiansebastian@MANUAL{RPROJECT, title = {R: A Language and Environment for Statistical Computing}, author = {{R Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org/}, } @ARTICLE{MALDIquant, title = {{MALDI}quant: a versatile {R} package for the analysis of mass spectrometry data}, author = {Sebastian Gibb and Korbinian Strimmer}, volume = {28}, number = {17}, pages = {2270-2271}, year = {2012}, doi = {10.1093/bioinformatics/bts447}, url = {http://bioinformatics.oxfordjournals.org/content/28/17/2270.abstract}, eprint = {http://bioinformatics.oxfordjournals.org/content/28/17/2270.full.pdf+html}, journal = {Bioinformatics}, publisher = {Oxford Univ Press}, } @ARTICLE{Tan2006, title={Finding regions of significance in {SELDI} measurements for identifying protein biomarkers}, author={Tan, Chuen Seng and Ploner, Alexander and Quandt, Andreas and Lehti{\"o}, Janne and Pawitan, Yudi}, volume={22}, number={12}, pages={1515--1523}, year={2006}, doi = {10.1093/bioinformatics/btl106}, url = {http://bioinformatics.oxfordjournals.org/content/22/12/1515.abstract}, eprint = {http://bioinformatics.oxfordjournals.org/content/22/12/1515.full.pdf+html}, journal={Bioinformatics}, publisher={Oxford Univ Press} } MALDIquantForeign/vignettes/MALDIquantForeign-intro.Rnw0000644000175000017500000001370412347107055024046 0ustar sebastiansebastian%\VignetteEngine{knitr} %\VignetteIndexEntry{MALDIquantForeign: Import/Export routines for MALDIquant} %\VignetteKeywords{Bioinformatics, Proteomics, Mass Spectrometry} %\VignettePackage{MALDIquantForeign} \documentclass[12pt]{article} \usepackage{natbib} \usepackage{hyperref} \usepackage{tikz} \usepackage{bibentry} % inline bibentries \nobibliography* % no special bibliography for bibentry \newcommand{\R}{\texttt{R}} \newcommand{\CRAN}{\texttt{CRAN}} \newcommand{\Rfunction}[1]{{\texttt{#1}}} \newcommand{\Robject}[1]{{\texttt{#1}}} \newcommand{\Rpackage}[1]{{\texttt{#1}}} \newcommand{\Mq}{\Rpackage{MALDIquant}} \newcommand{\MqF}{\Rpackage{MALDIquantForeign}} \newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}} \title{\MqF{}: Import/Export routines for \Mq{}} \author{ Sebastian Gibb% \thanks{\email{mail@sebastiangibb.de}} } \date{\today} \begin{document} <>= library("knitr") opts_chunk$set(tidy.opts=list(width.cutoff=45), tidy=FALSE, fig.align="center", fig.height=4.25, comment=NA, prompt=TRUE) @ <>= suppressPackageStartupMessages(library("MALDIquant")) suppressPackageStartupMessages(library("MALDIquantForeign")) @ \maketitle \begin{abstract} \MqF{} provides routines for importing/exporting different file formats into/from \Mq{}.\\ This vignette describes the usage of the \MqF{} package. \end{abstract} \clearpage \tableofcontents \section*{Foreword} \MqF{} is free and open source software for the \R{} \citep{RPROJECT} environment and under active development. If you use it, please support the project by citing it in publications: \begin{quote} \bibentry{MALDIquant} \end{quote} If you have any questions, bugs, or suggestions do not hesitate to contact me (\email{mail@sebastiangibb.de}). \\ Please visit \url{http://strimmerlab.org/software/maldiquant/}. \section{Introduction} \Mq{} should be device and platform independent. That's why it has not any import/export functions. \\ \MqF{} fills this gap and provides import/export routines for various file formats: <>= supportedFileFormats() @ \section{Setup} After starting \R{} we could install \Mq{} and \MqF{} directly from \CRAN{} using \Rfunction{install.packages}: <>= install.packages(c("MALDIquant", "MALDIquantForeign")) @ Before we can use \Mq{} and \MqF{} we have to load the packages. <>= library("MALDIquant") library("MALDIquantForeign") @ \section{Import} \MqF{} provides an \Rfunction{import} function that tries to auto-detect the correct file type. Because this would never be perfect \MqF{} offers also many \Rfunction{import*} functions like \Rfunction{importBrukerFlex}, \Rfunction{importMzMl}, etc. Please see the manual page of \Rfunction{import} for a complete list (\Rfunction{?import}).\\ First we try to import some example data in Bruker Daltonics *flex-series file format using the \Rfunction{import} function. <>= ## get the example directory exampleDirectory <- system.file("exampledata", package="MALDIquantForeign") spectra <- import(file.path(exampleDirectory, "brukerflex"), verbose=FALSE) spectra[[1]] @ Next we use the \Rfunction{importBrukerFlex} function (the result is the same as above). <>= spectra <- importBrukerFlex(file.path(exampleDirectory, "brukerflex"), verbose=FALSE) spectra[[1]] @ \MqF{} supports compressed files, too (\emph{zip}, \emph{tar.\{bz2, gz,xz\}}). <>= spectra <- importCsv(file.path(exampleDirectory, "compressed", "csv.tar.gz"), verbose=FALSE) spectra[[1]] spectra <- importCsv(file.path(exampleDirectory, "compressed", "csv.zip"), verbose=FALSE) spectra[[1]] @ Remote files are supported as well. Data are taken from \citet{Tan2006}. <>= spectra <- import(paste0("http://www.meb.ki.se/", "~yudpaw/papers/spikein_xml.zip"), centroided=FALSE, verbose=TRUE) @ If you want to read peak lists (centroided data) instead of spectra data you have to set \Rfunction{centroided=TRUE}. <>= peaks <- import(file.path(exampleDirectory, "ascii.txt"), centroided=TRUE, verbose=FALSE) peaks @ \section{Export} The export routines in \MqF{} are very similar to the import routines. Please see manual page of \Rfunction{export} for a complete list of supported export routines (\Rfunction{?export}). First we create a simple list of \Robject{MassSpectrum} objects using \Rfunction{createMassSpectrum}. <>= spectra <- list( createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=6:10)) @ Now we want to export the first spectrum into a CSV file. <>= export(spectra[[1]], file="spectrum1.csv") import("spectrum1.csv") @ Exporting every file by hand is cumbersome. We want to export the whole list of spectra. Instead of \Robject{file} we use \Robject{path} now to specify a directory. Please note that we have to add the file type/format information now (we can use the \Robject{type} argument or the corresponding \Rfunction{export*} function). If the path doesn't exists we will get an error. To force \Rfunction{export} to create/overwrite the given path, we set the argument \Robject{force=TRUE}. <>= export(spectra, type="csv", path="spectra", force=TRUE) list.files("spectra") @ \section{Analyse Mass Spectrometry Data} Please have a look at the corresponding vignette shipped with \Mq{} and the \Mq{} website: \url{http://strimmerlab.org/software/maldiquant/}. <>= vignette(topic="MALDIquant", package="MALDIquant") @ \section{Session Information} <>= toLatex(sessionInfo(), locale=FALSE) @ \bibliographystyle{apalike} \bibliography{bibliography} \end{document} MALDIquantForeign/DESCRIPTION0000644000175000017500000000225512615440602016505 0ustar sebastiansebastianPackage: MALDIquantForeign Version: 0.10.1 Date: 2015-11-01 Title: Import/Export Routines for MALDIquant Authors@R: c(person("Sebastian", "Gibb", role=c("aut", "cre"), email="mail@sebastiangibb.de"), person("Pietro", "Franceschi", role=c("ctb"), email="pietro.franceschi@fmach.it")) Depends: R (>= 3.2.2), methods, MALDIquant (>= 1.11.7) Imports: base64enc, digest, readBrukerFlexData (>= 1.7), readMzXmlData (>= 2.7), XML Suggests: knitr, testthat (>= 0.8), RNetCDF (>= 1.6.1) Description: Functions for reading (tab, csv, Bruker fid, Ciphergen XML, mzXML, mzML, imzML, Analyze 7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file formats of mass spectrometry data into/from MALDIquant objects. License: GPL (>= 3) URL: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/MALDIquantForeign/ BugReports: https://github.com/sgibb/MALDIquantForeign/issues/ LazyLoad: yes VignetteBuilder: knitr RoxygenNote: 5.0.0.9000 NeedsCompilation: no Packaged: 2015-11-01 16:44:50 UTC; sebastian Author: Sebastian Gibb [aut, cre], Pietro Franceschi [ctb] Maintainer: Sebastian Gibb MALDIquantForeign/NEWS0000644000175000017500000002002012615437722015475 0ustar sebastiansebastianRELEASE HISTORY OF THE "MALDIquantForeign" PACKAGE ================================================== Version 0.10.1 [2015-11-01 Sun]: INTERNAL CHANGES - Rezip inst/compressed/csv.tar.gz using `gzip -n` to avoid lintian's package-contains-timestamped-gzip warning; see https://wiki.debian.org/ReproducibleBuilds for details. CHANGES IN MALDIquantForeign VERSION 0.10 [2015-10-31]: ------------------------------------------------------- IMPROVEMENTS * Add parallel support on unix-based platforms using the parallel package. All `import*` functions support the "mc.cores" argument (default is 1, means no parallel import). Please read also `?"MALDIquantForeign-parallel"`. * Add importer for .msd (mMass) files: `importMsd`. * Add basic export support for imzML files: `exportImzMl`. * `.importImzMl`: add "coordinates" argument to access specific spectra by their x, y coordinates within an imzML file; closes #14; affected functions: `import`, `importImzMl`. Thanks to Heath Patterson for this idea. MODIFICATIONS * Remove dependency "downloader". Since R 3.2.2 https is supported on all platforms by `base::download.file`. * Use "verbose = interactive()" in `import`. * Replace old imzML example files in inst/exampledata. * `exportMzMl`: improve documentation of the "path" argument. * `.importImzMl`: if the imzML file doesn't contain any UUID a warning is thrown instead of an error; affected functions: `import`, `importImzMl`. * `.importImzMl`: if the imzML file doesn't contain any checksum for its corresponding idb file a warning is thrown (before it was an error); affected functions: `import`, `importImzMl`. INTERNAL CHANGES * Import non-base functions/methods via NAMESPACE. * Use MALDIquant's new `coordinates` method. * Replace `require` by `requireNamespace` as suggested by "Writing R Extensions". * Rezip gzip'ed files using `gzip -n` to avoid lintian's package-contains-timestamped-gzip warning; see https://wiki.debian.org/ReproducibleBuilds for details. CHANGES IN MALDIquantForeign VERSION 0.9 [2014-08-11]: ------------------------------------------------------ IMPROVEMENTS * `.readAnalyzeIntensity`: allow to specify a mass range of interest to reduce memory usage while importing Analyze files; affected functions: `import`, `importAnalyze` * `importAnalyze`: use `as.double` after reading the image dimensions to avoid integer overflows in vector allocations (the Analyze 7.5 format specification limits the dimensions to integer). Thanks to Ken Frankel for reporting this problem. * `importImzMl`: add MD5 checksum support for imzML files. Thanks to Ken Frankel for reporting this problem. CHANGES IN MALDIquantForeign VERSION 0.8 [2014-06-16]: ------------------------------------------------------ MODIFICATIONS * `import`: set argument `centroided=FALSE` as default (was `NA` before). The automatically determination of profile/centroided data was too error prone. Now we read everything as profile data (use `centroided=TRUE` to read centroided data); affected functions: all `import` functions (e.g. `importBrukerFlex`, `importMzMl` ...). IMPROVEMENTS * `importAnalyze`: circumvent the limit of 32747 intensity values that is specified in the official Analyze 7.5 format. Thanks to Ken Frankel for reporting this problem. INTERNAL CHANGES * Fix VignetteIndexEntry. * Rename vignette output file from MALDIquantForeign.pdf to MALDIquantForeign-intro.pdf. * Check availability of the "RNetCDF" package in the `importCdf` man page to avoid build failures on CRAN. * Don't evaluate the remote import example in the vignette to avoid build failures on CRAN. CHANGES IN MALDIquantForeign VERSION 0.7 [2014-04-11]: ------------------------------------------------------ IMPROVEMENTS * Add vignette. INTERNAL CHANGES * Move tests into tests/testthat to adapt to testthat 0.8 and new CRAN policy; close #10. * Fix path of exampledata (needed because the test scripts moved to tests). CHANGES IN MALDIquantForeign VERSION 0.6 [2014-01-28]: ------------------------------------------------------ NEW FEATURES * Add basic import support for CDF files [contributed by Pietro Franceschi]; new function: `importCdf`. * `import`: add arguments "massRange" and "minIntensity" to limit import range; affected functions: all `import*` functions. * `import`: add argument "centroided" to allow import of centroided spectra as MassPeaks objects; affected functions: all `import*` functions. IMPROVEMENTS * Add "skip" argument to `.importCsv`, `.importTab`, `.autoSep` and `.autoHeader` to allow skipping first lines; affected functions: `import`, `importTxt`, `importTab`, `importCsv` BUG FIXES * `importAnalyze`: add support for ABSiex Analyze 7.5 files. Thanks to Pietro Franceschi for reporting this bug/odd behaviour. * `.importTab`: use `.autoSep` and `.autoHeader` (before they were used only by `.importCsv`); affected functions: `import`, `importTxt`, `importTab` * `.parseMzML`: fix assignment operation. Before all metaData of spectra were overwritten by the metaData of the last spectrum (affected only mzML files with more than one spectrum). affected functions: `importMzML` * `export`: fix one file export; additional affected functions: `exportMzMl`. INTERNAL CHANGES * Regenerate man pages with new 'roxygen2' (3.0.0). CHANGES IN MALDIquantForeign VERSION 0.5.1 [2013-09-18]: -------------------------------------------------------- BUG FIXES * Replace MALDIquant:::isMassSpectrum by MALDIquant::isMassSpectrum. * Replace deprecated function isMassObjectList. CHANGES IN MALDIquantForeign VERSION 0.5 [2013-09-08]: ------------------------------------------------------ IMPROVEMENTS * `import*`: add "excludePattern" argument to avoid import of specific files; closes #8. BUGFIXES * Fix "totalIonCurrent" test case. * Add import("methods") to NAMESPACE (fixes #9). INTERNAL CHANGES * Update dependencies; now MALDIquantForeign depends on R 3.0.0. * Replace all paste(..., sep="") by paste0. CHANGES IN MALDIquantForeign VERSION 0.4 [2013-04-28]: ------------------------------------------------------ NEW FEATURES * Add basic import support for imzML files and Analyze 7.5 files. IMPROVEMENTS * `import`: add "removeEmptySpectra" argument; closes #7. MODIFICATIONS * `import`: change default argument "verbose" to TRUE. BUGFIXES * `.download`: respects "verbose" argument now (fixes #6). INTERNAL CHANGES * Remove LICENSE file. CHANGES IN MALDIquantForeign VERSION 0.3 [2013-03-01]: ------------------------------------------------------ NEW FEATURES * Add basic support for mzML export. * Add basic import support for Ciphergen XML files. * `import`: add http(s):// and ftp:// support. * `import`: add uncompression support to allow import of zip/tar.{gz,bz2,xz}-archives. BUGFIXES * Add missing "usage" section in `export` methods manual pages. * `.files`: returns only unique file names; affected functions: all import functions. INTERNAL CHANGES * `.make.unique`: generates c("a1", "a2") instead of c("a", "a1") and c("a001", ..., "a099", "a100") instead of c("a", ..., "a98", "a99"); affected method: `export,list`. * DESCRIPTION: move base64enc, digest, readBrukerFlexData, readMzXmlData and XML to "Imports". * DESCRIPTION: remove MALDIquant from the "Imports" field. CHANGES IN MALDIquantForeign VERSION 0.2 [2013-01-14]: ------------------------------------------------------ IMPROVEMENTS * `exportMsd`: complete rewrite, write xml files manually instead of using the XML package (increasing speed). BUGFIXES * `export`: fix empty filenames. * `export,list`: stop if directory doesn't exist. * `exportMsd`: fix peaks argument. * `exportMsd` tests: respect endianness. * `import`: respect verbose argument in `import(type="auto")`. CHANGES IN MALDIquantForeign VERSION 0.1 [2012-12-10]: ------------------------------------------------------ * First public release. * Supported file formats: * Import: tab, txt, csv, Bruker Daltonics *flex files, mzXML, mzML * Export: tab, csv, msd MALDIquantForeign/tests/0000755000175000017500000000000012523634224016140 5ustar sebastiansebastianMALDIquantForeign/tests/testthat.R0000644000175000017500000000006412523634224020123 0ustar sebastiansebastianlibrary("testthat") test_check("MALDIquantForeign") MALDIquantForeign/tests/testthat/0000755000175000017500000000000012615440675020007 5ustar sebastiansebastianMALDIquantForeign/tests/testthat/test_ibd-functions.R0000644000175000017500000000316512523634227023736 0ustar sebastiansebastiancontext("ibd") s <- list(createMassSpectrum(mass=1:5, intensity=1:5), createMassSpectrum(mass=1:5, intensity=6:10)) processed <- matrix(c(cumsum(c(16L, rep.int(40L, 3L))), rep.int(5L, 4L), rep.int(40L, 4L)), nrow=4L) continuous<- matrix(c(16L, 56L, 16L, 96L, rep.int(5L, 4L), rep.int(40L, 4L)), nrow=4L) dimnames(processed) <- dimnames(continuous) <- list(rep(c("mass", "intensity"), 2), c("offset", "length", "encodedLength")) test_that(".writeIbd", { #uuid <- "3858f622-30ac-4c91-9f30-0c664312c63f" #file <- tempfile() #MALDIquantForeign:::.writeIbd(filename=file, uuid=uuid) }) test_that(".ibdOffsets", { expect_identical(MALDIquantForeign:::.ibdOffsets(s, processed=TRUE), processed) expect_identical(MALDIquantForeign:::.ibdOffsets(s, processed=FALSE), continuous) }) test_that(".addIbdOffsets", { rp <- list(createMassSpectrum(mass=1:5, intensity=1:5, metaData=list(imaging=list(offsets=processed[1:2,]))), createMassSpectrum(mass=1:5, intensity=6:10, metaData=list(imaging=list(offsets=processed[3:4,])))) rc <- list(createMassSpectrum(mass=1:5, intensity=1:5, metaData=list(imaging=list(offsets=continuous[1:2,]))), createMassSpectrum(mass=1:5, intensity=6:10, metaData=list(imaging=list(offsets=continuous[3:4,])))) expect_identical(MALDIquantForeign:::.addIbdOffsets(s, processed=TRUE), rp) expect_identical(MALDIquantForeign:::.addIbdOffsets(s, processed=FALSE), rc) }) MALDIquantForeign/tests/testthat/test_importCiphergenXml-functions.R0000644000175000017500000000135712523634227027021 0ustar sebastiansebastiancontext("importCiphergenXml") test_that("importCiphergenXml", { expect_error(MALDIquantForeign:::.importCiphergenXml("tmp.tmp")) path <- system.file(file.path("exampledata", "ciphergen", "tiny.xml"), package="MALDIquantForeign") s <- MALDIquantForeign:::.importCiphergenXml(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importCiphergenXml(path, verbose=FALSE)) expect_equal(s, import(path, type="ciph", verbose=FALSE)) expect_equal(trunc(mass(s[[1]])), rep(26, 5)) expect_false(all(mass(s[[1]])[1] == mass(s[[1]]))) expect_equal(intensity(s[[1]]), 1:5) expect_equal(basename(metaData(s[[1]])$file), "tiny.xml") expect_equal(metaData(s[[1]])$name, "tiny example") }) MALDIquantForeign/tests/testthat/test_exportImzMl-methods.R0000644000175000017500000001752312523634227025130 0ustar sebastiansebastiancontext("exportImzMl") imzML <- c( "", "", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", paste0(" "), " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", "") test_that("exportImzMl", { tmp <- tempdir() m <- createMassSpectrum(mass=1:5, intensity=6:10, metaData=list(name="TEST", file="TESTS/fid")) expect_error(MALDIquantForeign:::.exportImzMl(m, file=file.path(tmp, "tmp.imzML")), "The spectra contain no imaging information.") MALDIquantForeign:::.exportImzMl(m, file=file.path(tmp, "tmp.imzML"), coordinates=cbind(1, 1), uuid="12345678-90ab-4cde-af12-34567890abcd") expect_equal(readLines(file.path(tmp, "tmp.imzML")), imzML) }) test_that("exportImzMl,list", { tmp <- tempdir() m <- createMassSpectrum(mass=1:5, intensity=6:10, metaData=list(name="TEST", file="TESTS/fid", imaging=list(pos=c(1, 1), pixelSize=c(100, 100), size=c(1, 1), dim=c(100, 100)))) spectra <- list(m, m) MALDIquantForeign::exportImzMl(spectra, path=tmp, force=TRUE, uuid="12345678-90ab-4cde-af12-34567890abcd") expect_equal(readLines(file.path(tmp, "TESTS_1.imzML")), sub(pattern="id=\"tmp\"", replacement="id=\"TESTS_1\"", x=imzML)) expect_equal(readLines(file.path(tmp, "TESTS_2.imzML")), sub(pattern="id=\"tmp\"", replacement="id=\"TESTS_2\"", x=imzML)) }) MALDIquantForeign/tests/testthat/test_importMzMl-functions.R0000644000175000017500000000543712601030514025300 0ustar sebastiansebastiancontext("importMzMl") test_that("importMzMl", { expect_error(MALDIquantForeign:::.importMzMl("tmp.tmp")) path <- normalizePath(system.file( file.path("exampledata", "tiny1.mzML1.1.mzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importMzMl(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importMzMl(path, verbose=FALSE)) expect_equal(s, import(path, type="mzML", verbose=FALSE)) expect_true(isMassSpectrum(s[[1]])) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny1.mzML1.1.mzML") expect_true(isMassSpectrum(s[[2]])) expect_equal(mass(s[[2]]), 1:5) expect_equal(intensity(s[[2]]), 10:6) expect_equal(basename(metaData(s[[2]])$file), "tiny1.mzML1.1.mzML") }) test_that("importMzMl compressed", { expect_error(MALDIquantForeign:::.importMzMl("tmp.tmp")) path <- normalizePath(system.file( file.path("exampledata", "tiny1-compressed.mzML1.1.mzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importMzMl(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importMzMl(path, verbose=FALSE)) expect_equal(s, import(path, type="mzML", verbose=FALSE)) expect_true(isMassSpectrum(s[[1]])) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny1-compressed.mzML1.1.mzML") expect_true(isMassSpectrum(s[[2]])) expect_equal(mass(s[[2]]), 1:5) expect_equal(intensity(s[[2]]), 10:6) expect_equal(basename(metaData(s[[2]])$file), "tiny1-compressed.mzML1.1.mzML") }) test_that("importMzMl centroided", { expect_error(MALDIquantForeign:::.importMzMl("tmp.tmp")) path <- normalizePath(system.file( file.path("exampledata", "tiny1-centroided.mzML1.1.mzML"), package="MALDIquantForeign")) p <- MALDIquantForeign:::.importMzMl(path, centroided=TRUE, verbose=FALSE) expect_equal(p, import(path, centroided=TRUE, verbose=FALSE)) expect_equal(p, importMzMl(path, centroided=TRUE, verbose=FALSE)) expect_equal(p, import(path, type="mzML", centroided=TRUE, verbose=FALSE)) expect_true(isMassPeaks(p[[1]])) expect_equal(mass(p[[1]]), 1:5) expect_equal(intensity(p[[1]]), 6:10) expect_equal(basename(metaData(p[[1]])$file), "tiny1-centroided.mzML1.1.mzML") expect_true(isMassPeaks(p[[2]])) expect_equal(mass(p[[2]]), 1:5) expect_equal(intensity(p[[2]]), 10:6) expect_equal(basename(metaData(p[[2]])$file), "tiny1-centroided.mzML1.1.mzML") ## overwrite default arguments path <- normalizePath(system.file( file.path("exampledata", "tiny1.mzML1.1.mzML"), package="MALDIquantForeign")) expect_true(all(sapply(MALDIquantForeign:::.importMzMl(path, centroided=TRUE), isMassPeaks))) }) MALDIquantForeign/tests/testthat/test_importMsd-functions.R0000644000175000017500000000114612523634227025153 0ustar sebastiansebastiancontext("importMsd") test_that("importMsd", { expect_error(MALDIquantForeign:::.importMsd("tmp.tmp")) path <- normalizePath(system.file( file.path("exampledata", "tiny1.msd"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importMsd(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importMsd(path, verbose=FALSE)) expect_equal(s, import(path, type="msd", verbose=FALSE)) expect_true(isMassSpectrum(s[[1]])) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny1.msd") }) MALDIquantForeign/tests/testthat/test_uuid-functions.R0000644000175000017500000000167412523634227024151 0ustar sebastiansebastiancontext("uuid") test_that(".uuid", { expect_identical(MALDIquantForeign:::.uuid(init="foobar"), "3858f622-30ac-4c91-9f30-0c664312c63f") }) test_that(".isUuidV4", { ## invalid letters (not hexadecimal) expect_false(MALDIquantForeign:::.isUuidV4("z858f622-30ac-4c91-9f30-0c664312c63f")) ## not version 4 expect_false(MALDIquantForeign:::.isUuidV4("3858f622-30ac-3c91-9f30-0c664312c63f")) ## y (pos 17 is not 8, 9, A, or B expect_false(MALDIquantForeign:::.isUuidV4("3858f622-30ac-4c91-cf30-0c664312c63f")) expect_true(MALDIquantForeign:::.isUuidV4("3858f622-30ac-4c91-9f30-0c664312c63f")) expect_true(MALDIquantForeign:::.isUuidV4("3858f62230ac4c919f300c664312c63f")) expect_true(MALDIquantForeign:::.isUuidV4(MALDIquantForeign:::.uuid())) expect_equal(MALDIquantForeign:::.isUuidV4(c("foobar", "3858f62230ac4c919f300c664312c63f")), c(FALSE, TRUE)) }) MALDIquantForeign/tests/testthat/test_exportTab-methods.R0000644000175000017500000000164412523634227024603 0ustar sebastiansebastiancontext("exportTab") m <- createMassSpectrum(mass=1:5, intensity=6:10) r <- data.frame(V1=1:5, V2=6:10) test_that("exportTab", { temp <- tempfile() MALDIquantForeign:::.exportTab(m, file=temp) ## didn't work on win-builder.r-project.org ## (but on local linux and windows install (both R 2.15.2) #expect_equivalent(tools::md5sum(temp), tools::md5sum(file.path("data", # "ascii.txt"))) expect_equal(read.table(temp), r) }) test_that("exportCsv", { temp <- tempfile() MALDIquantForeign:::.exportCsv(m, file=temp) ## didn't work on win-builder.r-project.org ## (but on local linux and windows install (both R 2.15.2) #expect_equivalent(tools::md5sum(temp), tools::md5sum(file.path("data", # "csv1.csv"))) colnames(r) <- c("mass", "intensity") expect_equal(read.csv(temp), r) }) MALDIquantForeign/tests/testthat/test_importBrukerFlex-functions.R0000644000175000017500000000135312523634227026501 0ustar sebastiansebastiancontext("importBrukerFlex") test_that("importBrukerFlex", { expect_error(MALDIquantForeign:::.importBrukerFlex("tmp.tmp")) path <- system.file( file.path("exampledata", "brukerflex", "0_A1", "1", "1SLin", "fid"), package="MALDIquantForeign") s <- MALDIquantForeign:::.importBrukerFlex(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importBrukerFlex(path, verbose=FALSE)) expect_equal(s, import(path, type="fid", verbose=FALSE)) expect_equal(trunc(mass(s[[1]])), 226:230) expect_equal(intensity(s[[1]]), 1:5) expect_equal(basename(metaData(s[[1]])$file), "fid") expect_equal(metaData(s[[1]])$laserShots, 100) expect_equal(metaData(s[[1]])$comments, paste0("TESTSAMPLE", 1:4)) }) MALDIquantForeign/tests/testthat/test_testChecksum-functions.R0000644000175000017500000000145112523634227025636 0ustar sebastiansebastiancontext("testChecksum") test_that("testChecksum-functions", { f <- normalizePath(system.file( file.path("exampledata", "ascii.txt"), package="MALDIquantForeign")) md5 <- "9274dd34d675950326a222a952309a17" sha1 <- "85572c8d56504d8bba2afb32d7d7df35fb127ab8" expect_true(MALDIquantForeign:::.testChecksum(f, md5, algo="md5")) expect_true(MALDIquantForeign:::.testChecksum(f, sha1, algo="sha1")) expect_false(suppressWarnings( MALDIquantForeign:::.testChecksum(f, "12345", algo="sha1"))) expect_warning(MALDIquantForeign:::.testChecksum(f, "12345", algo="sha1"), "Stored and calculated sha1 sums do not match") expect_warning(MALDIquantForeign:::.testChecksum(f, "12345", algo="md5"), "Stored and calculated md5 sums do not match") }) MALDIquantForeign/tests/testthat/test_msg-functions.R0000644000175000017500000000041612523634227023762 0ustar sebastiansebastiancontext("msg") test_that("msg-functions", { expect_message(MALDIquantForeign:::.msg(TRUE, "foobar"), "foobar") expect_message(MALDIquantForeign:::.msg(TRUE, "foo", "bar"), "foobar") expect_that(MALDIquantForeign:::.msg(FALSE, "foobar"), not(shows_message())) }) MALDIquantForeign/tests/testthat/test_sanitize-functions.R0000644000175000017500000000030712523634227025021 0ustar sebastiansebastiancontext("sanitize") test_that("sanitize-functions", { s <- c("ac", "a&o", "abc") r <- c("a<b", "b>c", "a&o", "abc") expect_identical(MALDIquantForeign:::.sanitize(s), r) }) MALDIquantForeign/tests/testthat/test_fileFormats.R0000644000175000017500000000075612523634227023450 0ustar sebastiansebastiancontext("fileFormats") test_that("supportedFileFormats", { r <- list(import = c("txt", "tab", "csv", "fid", "ciphergen", "mzxml", "mzml", "imzml", "analyze", "cdf", "msd"), export = c("tab", "csv", "msd", "mzml", "imzml")) expect_identical(supportedFileFormats(), r) }) MALDIquantForeign/tests/testthat/test_importImzMl-functions.R0000644000175000017500000000444312523634227025463 0ustar sebastiansebastiancontext("importImzMl") test_that("importImzMl continuous", { expect_error(MALDIquantForeign:::.importImzMl("tmp.tmp")) path <- normalizePath(system.file( file.path("exampledata", "tiny_continuous.imzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importImzMl(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importImzMl(path, verbose=FALSE)) expect_equal(s, import(path, type="imzML", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny_continuous.imzML") expect_equal(mass(s[[2]]), 1:5) expect_equal(intensity(s[[2]]), 10:6) expect_equal(basename(metaData(s[[2]])$file), "tiny_continuous.imzML") }) test_that("importImzMl processed", { path <- normalizePath(system.file( file.path("exampledata", "tiny_processed.imzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importImzMl(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importImzMl(path, verbose=FALSE)) expect_equal(s, import(path, type="imzML", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny_processed.imzML") expect_equal(mass(s[[2]]), 6:10) expect_equal(intensity(s[[2]]), 10:6) expect_equal(basename(metaData(s[[2]])$file), "tiny_processed.imzML") }) test_that("importImzMl coordinates", { path <- normalizePath(system.file( file.path("exampledata", "tiny_continuous.imzML"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importImzMl(path, verbose=FALSE) expect_equal(s, importImzMl(path, coordinates=cbind(1:2, c(1, 1)), verbose=FALSE)) expect_equal(s[1], importImzMl(path, coordinates=cbind(1, 1), verbose=FALSE)) expect_equal(s[[2]], importImzMl(path, coordinates=cbind(2, 1), verbose=FALSE)[[1]]) expect_error(importImzMl(path, coordinates=3, verbose=FALSE), "The .*coordinates.* argument has to be a matrix with two columns") expect_warning(importImzMl(path, coordinates=cbind(1:3, 2:0), verbose=FALSE), "The following rows contain invalid coordinates: 1, 3") }) MALDIquantForeign/tests/testthat/test_filename-functions.R0000644000175000017500000000520012523634227024750 0ustar sebastiansebastiancontext("filename") test_that(".cleanFilename", { expect_identical(MALDIquantForeign:::.cleanFilename( "/home/a:/\"foo&bar\"/g.\\23!/ foo-bar?.txt"), "_home_a_foo_bar_g_23_foo_bar_txt") }) test_that("file extension is returned", { expect_identical(MALDIquantForeign:::.fileExtension("~/foo.txt"), "txt") expect_identical(MALDIquantForeign:::.fileExtension( c("/etc/a.conf", "b.pdf")), c("conf", "pdf")) }) test_that("file name is returned", { expect_identical(MALDIquantForeign:::.fileExtension("~/foo"), "foo") }) test_that("path without extension is returned", { expect_identical(MALDIquantForeign:::.withoutFileExtension( c("~/foo", "/home/user/xyz.tar.gz", "/tmp/bar.txt")), c("~", "/home/user/xyz", "/tmp/bar")) }) test_that("file extension is changed", { expect_identical(MALDIquantForeign:::.changeFileExtension( c("/home/user/xyz.tar.gz", "/tmp/bar.txt"), c("txt", "csv")), c("/home/user/xyz.txt", "/tmp/bar.csv")) }) test_that(".cutFilenames", { expect_identical(MALDIquantForeign:::.cutFilenames( c("/home/user/foo.bar", "/home/user/xyz.tar.gz")), c("foo.bar", "xyz.tar.gz")) expect_identical(MALDIquantForeign:::.cutFilenames( c("/home/user/foo.bar", "/home/user/foo.bar")), c("foo.bar", "foo.bar")) }) test_that(".composeFilenames", { s <- createMassSpectrum(mass=1:5, intensity=1:5, metaData=list(file="/foo/bar.txt")) expect_identical(MALDIquantForeign:::.composeFilename(s), "/foo/bar.csv") expect_identical(MALDIquantForeign:::.composeFilename(s, fileExtension="xml"), "/foo/bar.xml") metaData(s) <- list(fullName="foo") expect_identical(MALDIquantForeign:::.composeFilename(s), "foo.csv") metaData(s) <- list(fullName=c("foo", "bar")) expect_identical(MALDIquantForeign:::.composeFilename(s), "foo_bar.csv") }) test_that(".uniqueBaseFilenames", { expect_identical(MALDIquantForeign:::.uniqueBaseFilenames( c("/home/user/foo.bar", "/home/user/foo.bar"), fileExtension="txt"), c("foo_1.txt", "foo_2.txt")) }) test_that(".make.unique", { expect_equal(MALDIquantForeign:::.make.unique(LETTERS[1:5]), LETTERS[1:5]) expect_equal(MALDIquantForeign:::.make.unique(rep(LETTERS[1:5], each=2)), paste(rep(LETTERS[1:5], each=2), 1:2, sep="_")) expect_equal(MALDIquantForeign:::.make.unique(rep(LETTERS[1:2], each=10)), sprintf("%s_%02d", rep(LETTERS[1:2], each=10), 1:10)) }) MALDIquantForeign/tests/testthat/test_exportMsd-methods.R0000644000175000017500000000403612523634227024616 0ustar sebastiansebastiancontext("exportMsd") m <- createMassSpectrum(mass=1:5, intensity=6:10, metaData=list(owner="OWNER", institution="INSTITUTION", instrument="INSTRUMENT")) p <- createMassPeaks(mass=4:5, intensity=9:10, snr=1:2) msd <- c( "", "", " ", " tmp.msd", " ", " ", " ", " ", " ", " ", " ", " ", " eJxjYACBD/YMEOAAoTigtACUFnEAADZ/Alw=", " eJxjYAABCQcwxSADpRWgtBKUVnEAAB9MAds=", " ", " ", " ", " ", " ", "") if (.Platform$endian == "big") { msd[13:14] <- c( " eJyz/8AABg4MUJoDSgtAaREIDQBExAJc", " eJxzkGAAAwcZKK0ApZWgtAqEBgArDgHb") } test_that("exportMsd", { tmp <- tempdir() MALDIquantForeign:::.exportMsd(m, file=file.path(tmp, "tmp.msd"), peaks=p) expect_equal(readLines(file.path(tmp, "tmp.msd"))[-c(4, 5)], msd[-c(4, 5)]) }) test_that("exportMsd,list", { tmp <- tempdir() spectra <- list(m, m) peaks <- list(p, p) MALDIquantForeign::exportMsd(spectra, path=tmp, force=TRUE, peaks=peaks) expect_equal(readLines(file.path(tmp, "1.msd"))[-c(4, 5)], msd[-c(4, 5)]) expect_equal(readLines(file.path(tmp, "2.msd"))[-c(4, 5)], msd[-c(4, 5)]) }) test_that(".createMsdTitle", { f <- file(file.path(tempdir(), "test.msd")) expect_true(MALDIquantForeign:::.createMsdTitle(f) == "test") close(f) }) MALDIquantForeign/tests/testthat/test_importMzXml-functions.R0000644000175000017500000000400512523634227025474 0ustar sebastiansebastiancontext("importMzXml") test_that("importMzXml", { expect_error(MALDIquantForeign:::.importMzXml("tmp.tmp")) path <- system.file(file.path("exampledata", "tiny1.mzXML3.0.mzXML"), package="MALDIquantForeign") s <- MALDIquantForeign:::.importMzXml(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importMzXml(path, verbose=FALSE)) expect_equal(s, import(path, type="mzXML", verbose=FALSE)) expect_true(isMassSpectrum(s[[1]])) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny1.mzXML3.0.mzXML") }) test_that("importMzXml compressed", { expect_error(MALDIquantForeign:::.importMzXml("tmp.tmp")) path <- system.file(file.path("exampledata", "tiny1-compressed.mzXML3.0.mzXML"), package="MALDIquantForeign") s <- MALDIquantForeign:::.importMzXml(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importMzXml(path, verbose=FALSE)) expect_equal(s, import(path, type="mzXML", verbose=FALSE)) expect_true(isMassSpectrum(s[[1]])) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "tiny1-compressed.mzXML3.0.mzXML") }) test_that("importMzXml centroided", { expect_error(MALDIquantForeign:::.importMzXml("tmp.tmp")) path <- system.file(file.path("exampledata", "tiny1-centroided.mzXML3.0.mzXML"), package="MALDIquantForeign") p <- MALDIquantForeign:::.importMzXml(path, centroided=TRUE, verbose=FALSE) expect_equal(p, import(path, centroided=TRUE, verbose=FALSE)) expect_equal(p, importMzXml(path, centroided=TRUE, verbose=FALSE)) expect_equal(p, import(path, type="mzXML", centroided=TRUE, verbose=FALSE)) expect_true(isMassPeaks(p[[1]])) expect_equal(mass(p[[1]]), 1:5) expect_equal(intensity(p[[1]]), 6:10) expect_equal(basename(metaData(p[[1]])$file), "tiny1-centroided.mzXML3.0.mzXML") }) MALDIquantForeign/tests/testthat/test_createMassObject-functions.R0000644000175000017500000000340112601026330026372 0ustar sebastiansebastiancontext("createMassObject") test_that(".createMassObject", { expect_true(isMassSpectrum( MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, metaData=list()))) expect_true(isMassSpectrum( MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, metaData=list(), centroided=FALSE))) expect_warning(MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, metaData=list(dataProcessing=list(centroided=0)), centroided=TRUE), paste0("According to the metadata information the imported data are ", "not centroided.")) expect_warning(MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, metaData=list(centroided="1")), paste0("According to the metadata information the imported data are ", "centroided.")) expect_true(suppressWarnings(isMassPeaks( MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, metaData=list(), centroided=TRUE)))) expect_true(suppressWarnings(isMassPeaks( MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, metaData=list(dataProcessing=list(centroided="1")), centroided=TRUE)))) expect_true(isMassSpectrum( MALDIquantForeign:::.createMassObject( mass=c(1, 5, 7), intensity=1:3, metaData=list()))) expect_equal(mass(MALDIquantForeign:::.createMassObject( mass=1:10, intensity=1:10, massRange=c(4, 8))), 4:8) expect_equal(intensity(MALDIquantForeign:::.createMassObject( mass=1:10, intensity=1:10, minIntensity=5)), 5:10) expect_equal(snr(MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, snr=5:1, centroided=TRUE)), 5:1) expect_equal(snr(MALDIquantForeign:::.createMassObject( mass=1:5, intensity=1:5, centroided=TRUE)), rep(NA_real_, 5)) }) MALDIquantForeign/tests/testthat/test_exportMzMl-methods.R0000644000175000017500000001067412523634227024757 0ustar sebastiansebastiancontext("exportMzMl") m <- createMassSpectrum(mass=1:5, intensity=6:10, metaData=list(name="TEST", file="TESTS/fid")) mzML <- c( "", "", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", paste0(" "), " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " eJxjYACBD/YMEOAAoTigtACUFnEAADZ/Alw=", " ", " ", " ", " ", " ", " eJxjYAABCQcwxSADpRWgtBKUVnEAAB9MAds=", " ", " ", " ", " ", " ", "") test_that("exportMzMl", { tmp <- tempdir() MALDIquantForeign:::.exportMzMl(m, file=file.path(tmp, "tmp.mzML")) expect_equal(readLines(file.path(tmp, "tmp.mzML")), mzML) g <- readLines(file.path(tmp, "tmp.mzML")) }) test_that("exportMzMl,list", { tmp <- tempdir() spectra <- list(m, m) MALDIquantForeign::exportMzMl(spectra, path=tmp, force=TRUE) expect_equal(readLines(file.path(tmp, "TESTS_1.mzML")), sub(pattern="id=\"tmp\"", replacement="id=\"TESTS_1\"", x=mzML)) expect_equal(readLines(file.path(tmp, "TESTS_2.mzML")), sub(pattern="id=\"tmp\"", replacement="id=\"TESTS_2\"", x=mzML)) }) MALDIquantForeign/tests/testthat/test_compression-functions.R0000644000175000017500000000614512523634227025542 0ustar sebastiansebastiancontext("compression") z <- c("bz2", "bzip2", "gz", "lzma", "xz") e <- c("zip", z, paste("tar", z, sep="."), "tar", "txt", "mzML") f <- paste(letters[1:13], e, sep=".") test_that(".isCompressed", { expect_identical(MALDIquantForeign:::.isCompressed(f), c(rep(TRUE, 11), rep(FALSE, 3))) }) test_that(".isTar", { expect_identical(MALDIquantForeign:::.isTar(f), c(rep(FALSE, 6), rep(TRUE, 6), rep(FALSE, 2))) }) test_that(".isZip", { expect_identical(MALDIquantForeign:::.isZip(f), c(TRUE, rep(FALSE, 13))) }) test_that(".isPackedOrCompressed", { expect_identical(MALDIquantForeign:::.isPackedOrCompressed(f), c(rep(TRUE, 12), rep(FALSE, 2))) }) test_that(".uncompress supports single file compression by gunzip", { u <- MALDIquantForeign:::.uncompress( system.file(file.path("exampledata", "compressed", "csv1.csv.gz"), package="MALDIquantForeign")) f <- system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign") expect_identical(readLines(u), readLines(f)) expect_identical(MALDIquantForeign:::.uncompress("foobar.txt"), "foobar.txt") expect_error(MALDIquantForeign:::.uncompress("foobar.gz"), ".*foobar.gz.* doesn't exist!") }) test_that(".uncompress supports tar compression by untar", { u <- list.files(MALDIquantForeign:::.uncompress( system.file( file.path("exampledata", "compressed", "csv.tar.gz"), package="MALDIquantForeign")), recursive=TRUE, pattern="^.*\\.csv$", full.names=TRUE)[1] f <- system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign") expect_identical(readLines(u), readLines(f)) }) test_that(".uncompress supports zip compression by unzip", { u <- list.files(MALDIquantForeign:::.uncompress( system.file( file.path("exampledata", "compressed", "csv.zip"), package="MALDIquantForeign")), recursive=TRUE, pattern="^.*\\.csv$", full.names=TRUE)[1] f <- system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign") expect_identical(readLines(u), readLines(f)) expect_error(MALDIquantForeign:::.uncompress("foobar.zip"), "unzip failed!") }) test_that(".cleanupUncompressedTmpFiles works", { n <- list.files(file.path(tempdir(), "MALDIquantForeign_uncompress"), recursive=TRUE) expect_true(length(n) > 0) MALDIquantForeign:::.cleanupUncompressedTmpFiles() expect_false(file.exists(file.path(tempdir(), "MALDIquantForeign_uncompress"))) }) test_that("typical auto import", { f <- normalizePath(system.file( file.path("exampledata", "compressed", "csv1.csv.gz"), package="MALDIquantForeign")) s <- createMassSpectrum(mass=1:5, intensity=6:10) i <- import(f)[[1]] metaData(i) <- list() expect_identical(i, s) expect_false(file.exists(file.path(tempdir(), "MALDIquantForeign_uncompress"))) }) MALDIquantForeign/tests/testthat/test_list.files-functions.R0000644000175000017500000000167112615154055025252 0ustar sebastiansebastiancontext("list.files") test_that("list.files-functions", { path <- normalizePath(system.file("exampledata", package="MALDIquantForeign")) expect_identical(MALDIquantForeign:::.list.files(path, pattern="tiny1-c"), normalizePath(file.path(path, c("tiny1-centroided.mzML1.1.mzML", "tiny1-centroided.mzXML3.0.mzXML", "tiny1-compressed.mzML1.1.mzML", "tiny1-compressed.mzXML3.0.mzXML")))) expect_identical(MALDIquantForeign:::.list.files(path, pattern="tiny1-c", excludePattern="\\.mzXML$"), normalizePath(file.path(path, c("tiny1-centroided.mzML1.1.mzML", "tiny1-compressed.mzML1.1.mzML")))) }) MALDIquantForeign/tests/testthat/test_download-functions.R0000644000175000017500000000331112615126401024770 0ustar sebastiansebastiancontext("download") url <- c("http://www.tld.com/", "https://www.tld.com/archive.zip", "ftp://ftp.tld.com", "/data/archive.zip", "/root", "/dev/data.csv") test_that(".isUrl", { expect_identical(MALDIquantForeign:::.isUrl(url), c(rep(TRUE, 3), rep(FALSE, 3))) }) test_that(".download", { skip_on_cran() skip_on_travis() urls <- c("https://raw.githubusercontent.com/sgibb/MALDIquantForeign/master/inst/exampledata/ascii.txt", "https://raw.githubusercontent.com/sgibb/MALDIquantForeign/master/inst/exampledata/csv1.csv") tmpdir <- tempdir() ascii <- data.frame(V1=1:5, V2=6:10) csv <- data.frame(mass=1:5, intensity=6:10) expect_identical(read.table( MALDIquantForeign:::.download(urls[1], file.path(tmpdir, "a.txt"))), ascii) expect_identical(read.table(MALDIquantForeign:::.download(urls[1])), ascii) expect_true(all(grepl(paste("^a\\.txt$", "^MALDIquantForeign_download/ascii_.*\\.txt$", "^MALDIquantForeign_download/csv1_.*\\.csv$", sep="|"), list.files(tmpdir, recursive=TRUE)))) files <- MALDIquantForeign:::.download(urls) expect_identical(list(read.table(files[1]), read.csv(files[2])), list(ascii, csv)) expect_message(MALDIquantForeign:::.download(urls[1], file.path(tmpdir, "a.txt"), verbose=TRUE), paste0("Downloading ", urls[1], " to ", file.path(tmpdir, "a.txt"), "\\.")) }) MALDIquantForeign/tests/testthat/test_importTab-functions.R0000644000175000017500000000551212523634227025137 0ustar sebastiansebastiancontext("importTab") test_that("importTab", { ## suppress warnings to avoid creation of Rplots.pdf expect_error(suppressWarnings(MALDIquantForeign:::.importTab("tmp.tmp"))) path <- normalizePath(system.file(file.path("exampledata", "ascii.txt"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importTab(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importTxt(path, verbose=FALSE)) expect_equal(s, import(path, type="txt", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "ascii.txt") }) test_that("importCsv", { ## suppress warnings to avoid creation of Rplots.pdf expect_error(suppressWarnings(MALDIquantForeign:::.importCsv("tmp.tmp"))) path <- normalizePath(system.file(file.path("exampledata", "csv1.csv"), package="MALDIquantForeign")) s <- MALDIquantForeign:::.importCsv(path, sep=",", header=TRUE, verbose=FALSE) expect_equal(s, import(path, sep=",", header=TRUE, verbose=FALSE)) expect_equal(s, importCsv(path, sep=",", header=TRUE, verbose=FALSE)) expect_equal(s, import(path, type="csv", sep=",", header=TRUE, verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv1.csv") ## auto header s <- MALDIquantForeign:::.importCsv(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importCsv(path, verbose=FALSE)) expect_equal(s, import(path, type="csv", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv1.csv") s <- MALDIquantForeign:::.importCsv(system.file( file.path("exampledata", "csv2.csv"), package="MALDIquantForeign"), sep=";", header=FALSE) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv2.csv") ## auto header s <- MALDIquantForeign:::.importCsv(file.path(dirname(path), "csv2.csv"), sep=";") expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 6:10) expect_equal(basename(metaData(s[[1]])$file), "csv2.csv") }) x <- c("10, 30", "\"foo\", \"bar\"", "foo; bar", "foo\tbar", "1\t 2") sep <- c(",", ",", ";", "\t", "\t") test_that("autoHeader", { result <- c(FALSE, TRUE, TRUE, TRUE, FALSE) for (i in seq(along=x)) { expect_identical(MALDIquantForeign:::.autoHeader(textConnection(x[i]), sep=sep[i]), result[i]) } }) test_that("autoSep", { for (i in seq(along=x)) { expect_identical(MALDIquantForeign:::.autoSep(textConnection(x[i])), sep[i]) } }) MALDIquantForeign/tests/testthat/test_importCdf-functions.R0000644000175000017500000000416712523634227025132 0ustar sebastiansebastiancontext("importCdf") ## create NetCDF test file # #library("RNetCDF") #nc <- create.nc("tiny.cdf") # #dim.def.nc(nc, "scan_number", 2) #dim.def.nc(nc, "point_number", 10, unlim=TRUE) # #var.def.nc(nc, "scan_index", "NC_INT", "scan_number") #var.def.nc(nc, "point_count", "NC_INT", "scan_number") #var.def.nc(nc, "scan_acquisition_time", "NC_DOUBLE", "scan_number") # #var.def.nc(nc, "mass_values", "NC_DOUBLE", "point_number") #var.def.nc(nc, "intensity_values", "NC_INT", "point_number") # #var.put.nc(nc, "scan_index", c(0,5)) #var.put.nc(nc, "point_count", c(5, 5)) #var.put.nc(nc, "scan_acquisition_time", c(1, 2)) # #var.put.nc(nc, "mass_values", 1:5, start=1, count=5) #var.put.nc(nc, "mass_values", 6:10, start=6, count=5) #var.put.nc(nc, "intensity_values", 11:15, start=1, count=5) #var.put.nc(nc, "intensity_values", 16:20, start=6, count=5) # #close.nc(nc) # test_that("importCdf", { path <- normalizePath(system.file(file.path("exampledata", "tiny.cdf"), package="MALDIquantForeign")) if (suppressWarnings(require("RNetCDF", quietly=TRUE))) { ## suppress warnings to avoid creation of Rplots.pdf expect_error(suppressWarnings(MALDIquantForeign:::.importCdf("tmp.tmp"))) r <- list(createMassSpectrum(mass=1:5, intensity=11:15, metaData=list(file=path, number=1, retentionTime=1, scanIndex=0)), createMassSpectrum(mass=6:10, intensity=16:20, metaData=list(file=path, number=2, retentionTime=2, scanIndex=5))) s <- MALDIquantForeign:::.importCdf(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importCdf(path, verbose=FALSE)) expect_equal(s, import(path, type="cdf", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 11:15) expect_equal(basename(metaData(s[[1]])$file), "tiny.cdf") expect_equal(s, r) } else { expect_error(suppressWarnings(MALDIquantForeign:::.importCdf(path)), "install.packages") } }) MALDIquantForeign/build/0000755000175000017500000000000012615440602016072 5ustar sebastiansebastianMALDIquantForeign/build/vignette.rds0000644000175000017500000000043112615440602020427 0ustar sebastiansebastianRK0Ni*)0t06KFݛZ2G;B(a0dc43ԈdbvMV܂TR6]&^@oT{8ؕWF:^Y;Ge@'mJL 3YKSϠu;eAZxU.zi.s>ZFK-h<~B?t30q'σͳ EA6i#|٠*J:)iX5`KJ