@@ -81,8 +84,6 @@ #if $peaklist.peaklistBool - variableMetadataOutput '$variableMetadata' - dataMatrixOutput '$dataMatrix' convertRTMinute $peaklist.convertRTMinute numDigitsMZ $peaklist.numDigitsMZ numDigitsRT $peaklist.numDigitsRT @@ -108,10 +109,10 @@ - + (peaklist['peaklistBool']) - + (peaklist['peaklistBool']) @@ -131,6 +132,39 @@ + + +For details and explanations for all the parameters and the workflow of xcms_ package, see its manual_ and this example_ + +.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html +.. _manual: http://www.bioconductor.org/packages/release/bioc/manuals/xcms/man/xcms.pdf +.. _example: https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html + + + + + +Get a Peak List +--------------- + +If 'true', the module generates two additional files corresponding to the peak list: +- the variable metadata file (corresponding to information about extracted ions such as mass or retention time) +- the data matrix (corresponding to related intensities) + +**decimal places for [mass or retention time] values in identifiers** + + | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time. + | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively. + | Theses parameters do not affect decimal places in columns other than the identifier one. + +**Reported intensity values** + + | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter: + | - into: integrated area of original (raw) peak + | - maxo: maximum intensity of original (raw) peak + | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’) + + diff -r c013ed353a2f -r 4d6f4cd7c3ef test-data/faahKO-single-class.xset.group.RData Binary file test-data/faahKO-single-class.xset.group.RData has changed diff -r c013ed353a2f -r 4d6f4cd7c3ef test-data/faahKO.xset.group.RData Binary file test-data/faahKO.xset.group.RData has changed diff -r c013ed353a2f -r 4d6f4cd7c3ef xcms.r --- a/xcms.r Tue Feb 13 04:44:03 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,229 +0,0 @@ -#!/usr/bin/env Rscript -# xcms.r version="2.2.0" -#Authors ABIMS TEAM -#BPC Addition from Y.guitton - - -# ----- LOG FILE ----- -log_file=file("log.txt", open = "wt") -sink(log_file) -sink(log_file, type = "output") - - -# ----- PACKAGE ----- -cat("\tPACKAGE INFO\n") -#pkgs=c("xcms","batch") -pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "xcms","snow","batch") -for(pkg in pkgs) { - suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) - cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="") -} -source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } -cat("\n\n"); - - - - - -# ----- ARGUMENTS ----- -cat("\tARGUMENTS INFO\n") -listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects -write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t') - -cat("\n\n"); - - -# ----- ARGUMENTS PROCESSING ----- -cat("\tINFILE PROCESSING INFO\n") - -#image is an .RData file necessary to use xset variable given by previous tools -if (!is.null(listArguments[["image"]])){ - load(listArguments[["image"]]); listArguments[["image"]]=NULL -} - -#Import the different functions -source_local("lib.r") - -cat("\n\n") - -#Import the different functions - -# ----- PROCESSING INFILE ----- -cat("\tARGUMENTS PROCESSING INFO\n") - -# Save arguments to generate a report -if (!exists("listOFlistArguments")) listOFlistArguments=list() -listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments - - -#saving the commun parameters -thefunction = listArguments[["xfunction"]]; listArguments[["xfunction"]]=NULL #delete from the list of arguments - -xsetRdataOutput = paste(thefunction,"RData",sep=".") -if (!is.null(listArguments[["xsetRdataOutput"]])){ - xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL -} - -#saving the specific parameters -rplotspdf = "Rplots.pdf" -if (!is.null(listArguments[["rplotspdf"]])){ - rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL -} -sampleMetadataOutput = "sampleMetadata.tsv" -if (!is.null(listArguments[["sampleMetadataOutput"]])){ - sampleMetadataOutput = listArguments[["sampleMetadataOutput"]]; listArguments[["sampleMetadataOutput"]]=NULL -} -variableMetadataOutput = "variableMetadata.tsv" -if (!is.null(listArguments[["variableMetadataOutput"]])){ - variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL -} -dataMatrixOutput = "dataMatrix.tsv" -if (!is.null(listArguments[["dataMatrixOutput"]])){ - dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL -} -if (!is.null(listArguments[["convertRTMinute"]])){ - convertRTMinute = listArguments[["convertRTMinute"]]; listArguments[["convertRTMinute"]]=NULL -} -if (!is.null(listArguments[["numDigitsMZ"]])){ - numDigitsMZ = listArguments[["numDigitsMZ"]]; listArguments[["numDigitsMZ"]]=NULL -} -if (!is.null(listArguments[["numDigitsRT"]])){ - numDigitsRT = listArguments[["numDigitsRT"]]; listArguments[["numDigitsRT"]]=NULL -} -if (!is.null(listArguments[["intval"]])){ - intval = listArguments[["intval"]]; listArguments[["intval"]]=NULL -} - -if (thefunction %in% c("xcmsSet","retcor")) { - ticspdf = listArguments[["ticspdf"]]; listArguments[["ticspdf"]]=NULL - bicspdf = listArguments[["bicspdf"]]; listArguments[["bicspdf"]]=NULL -} - - -if (thefunction %in% c("xcmsSet","retcor","fillPeaks")) { - if (!exists("singlefile")) singlefile=NULL - if (!exists("zipfile")) zipfile=NULL - rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments) - zipfile = rawFilePath$zipfile - singlefile = rawFilePath$singlefile - listArguments = rawFilePath$listArguments - directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) - md5sumList=list("origin"=getMd5sum(directory)) -} - -#addition of the directory to the list of arguments in the first position -if (thefunction == "xcmsSet") { - checkXmlStructure(directory) - checkFilesCompatibilityWithXcms(directory) - listArguments=append(directory, listArguments) -} - - -#addition of xset object to the list of arguments in the first position -if (exists("xset")){ - listArguments=append(list(xset), listArguments) -} - -cat("\n\n") - - - - -# ----- MAIN PROCESSING INFO ----- -cat("\tMAIN PROCESSING INFO\n") - - -#Verification of a group step before doing the fillpeaks job. - -if (thefunction == "fillPeaks") { - res=try(is.null(groupnames(xset))) - if (class(res) == "try-error"){ - error<-geterrmessage() - write(error, stderr()) - stop("You must always do a group step after a retcor. Otherwise it won't work for the fillpeaks step") - } - -} - -#change the default display settings -#dev.new(file="Rplots.pdf", width=16, height=12) -pdf(file=rplotspdf, width=16, height=12) -if (thefunction == "group") { - par(mfrow=c(2,2)) -} -#else if (thefunction == "retcor") { -#try to change the legend display -# par(xpd=NA) -# par(xpd=T, mar=par()$mar+c(0,0,0,4)) -#} - - -#execution of the function "thefunction" with the parameters given in "listArguments" - -cat("\t\tCOMPUTE\n") -xset = do.call(thefunction, listArguments) - -# check if there are no peaks -if (nrow(peaks(xset)) == 0) { - stop("No peaks were detected. You should review your settings") -} - - -cat("\n\n") - -dev.off() #dev.new(file="Rplots.pdf", width=16, height=12) - -if (thefunction == "xcmsSet") { - - #transform the files absolute pathways into relative pathways - xset@filepaths<-sub(paste(getwd(),"/",sep="") ,"", xset@filepaths) - if(exists("zipfile") && !is.null(zipfile) && (zipfile!="")) { - - #Modify the samples names (erase the path) - for(i in 1:length(sampnames(xset))){ - - sample_name=unlist(strsplit(sampnames(xset)[i], "/")) - sample_name=sample_name[length(sample_name)] - sample_name= unlist(strsplit(sample_name,"[.]"))[1] - sampnames(xset)[i]=sample_name - - } - - } - -} - -# -- TIC -- -if (thefunction == "xcmsSet") { - cat("\t\tGET TIC GRAPH\n") - sampleNamesList = getSampleMetadata(xcmsSet=xset, sampleMetadataOutput=sampleMetadataOutput) - getTICs(xcmsSet=xset, pdfname=ticspdf,rt="raw") - getBPCs(xcmsSet=xset,rt="raw",pdfname=bicspdf) -} else if (thefunction == "retcor") { - cat("\t\tGET TIC GRAPH\n") - getTICs(xcmsSet=xset, pdfname=ticspdf,rt="corrected") - getBPCs(xcmsSet=xset,rt="corrected",pdfname=bicspdf) -} - -if ((thefunction == "group" || thefunction == "fillPeaks") && exists("intval")) { - getPeaklistW4M(xset,intval,convertRTMinute,numDigitsMZ,numDigitsRT,variableMetadataOutput,dataMatrixOutput) -} - - -cat("\n\n") - -# ----- EXPORT ----- - -cat("\tXSET OBJECT INFO\n") -print(xset) -#delete the parameters to avoid the passage to the next tool in .RData image - - -#saving R data in .Rdata file to save the variables used in the present tool -objects2save = c("xset","zipfile","singlefile","listOFlistArguments","md5sumList","sampleNamesList") -save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput) - -cat("\n\n") - - -cat("\tDONE\n") diff -r c013ed353a2f -r 4d6f4cd7c3ef xcms_retcor.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xcms_retcor.r Thu Mar 01 04:16:45 2018 -0500 @@ -0,0 +1,106 @@ +#!/usr/bin/env Rscript + +# ----- LOG FILE ----- +log_file=file("log.txt", open = "wt") +sink(log_file) +sink(log_file, type = "output") + + +# ----- PACKAGE ----- +cat("\tSESSION INFO\n") + +#Import the different functions +source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } +source_local("lib.r") + +pkgs <- c("xcms","batch","RColorBrewer") +loadAndDisplayPackages(pkgs) +cat("\n\n"); + + +# ----- ARGUMENTS ----- +cat("\tARGUMENTS INFO\n") +args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects +write.table(as.matrix(args), col.names=F, quote=F, sep='\t') + +cat("\n\n") + +# ----- PROCESSING INFILE ----- +cat("\tARGUMENTS PROCESSING INFO\n") + +#saving the specific parameters +method <- args$method; args$method <- NULL + +cat("\n\n") + + +# ----- ARGUMENTS PROCESSING ----- +cat("\tINFILE PROCESSING INFO\n") + +#image is an .RData file necessary to use xset variable given by previous tools +load(args$image); args$image=NULL +if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*") + +# Handle infiles +if (!exists("singlefile")) singlefile <- NULL +if (!exists("zipfile")) zipfile <- NULL +rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) +zipfile <- rawFilePath$zipfile +singlefile <- rawFilePath$singlefile +args <- rawFilePath$args +directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile) + +# Check some character issues +md5sumList <- list("origin" = getMd5sum(directory)) +checkXmlStructure(directory) +checkFilesCompatibilityWithXcms(directory) + + +cat("\n\n") + + +# ----- MAIN PROCESSING INFO ----- +cat("\tMAIN PROCESSING INFO\n") + + +cat("\t\tCOMPUTE\n") + +cat("\t\t\tAlignment/Retention Time correction\n") +adjustRtimeParam <- do.call(paste0(method,"Param"), args) +print(adjustRtimeParam) +xdata <- adjustRtime(xdata, param=adjustRtimeParam) + +# Get the legacy xcmsSet object +xset <- getxcmsSetObject(xdata) + +cat("\n\n") + + +# -- TIC -- +cat("\t\tDRAW GRAPHICS\n") +getPlotAdjustedRtime(xdata) + +#@TODO: one day, use xdata instead of xset to draw the TICs and BPC or a complete other method +getTICs(xcmsSet=xset, rt="raw", pdfname="TICs.pdf") +getBPCs(xcmsSet=xset, rt="raw", pdfname="BICs.pdf") + +cat("\n\n") + +# ----- EXPORT ----- + +cat("\tXCMSnExp OBJECT INFO\n") +print(xdata) +cat("\n\n") + +cat("\txcmsSet OBJECT INFO\n") +print(xset) +cat("\n\n") + +#saving R data in .Rdata file to save the variables used in the present tool +objects2save = c("xdata","zipfile","singlefile","md5sumList","sampleNamesList") +save(list=objects2save[objects2save %in% ls()], file="retcor.RData") + +cat("\n\n") + + +cat("\tDONE\n")