xcms_summary: lib.r annotate

annotate lib.r @ 31:0b5521b78c92 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

author	lecorguille
date	Thu, 08 Mar 2018 05:55:26 -0500
parents	17562a6799a1
children	de3b88417327

rev	line source
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	1 #@authors ABiMS TEAM, Y. Guitton
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	2 # lib.r for Galaxy Workflow4Metabolomics xcms tools
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	3
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	4 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	5 # solve an issue with batch if arguments are logical TRUE/FALSE
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	6 parseCommandArgs <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	7 args <- batch::parseCommandArgs(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	8 for (key in names(args)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	9 if (args[key] %in% c("TRUE","FALSE"))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	10 args[key] = as.logical(args[key])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	11 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	12 return(args)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	13 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	14
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	15 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	16 # This function will
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	17 # - load the packages
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	18 # - display the sessionInfo
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	19 loadAndDisplayPackages <- function(pkgs) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	20 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	21
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	22 sessioninfo = sessionInfo()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	23 cat(sessioninfo$R.version$version.string,"\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	24 cat("Main packages:\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	25 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	26 cat("Other loaded packages:\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	27 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	28 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	29
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	30 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	31 # This function convert if it is required the Retention Time in minutes
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	32 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	33 if (convertRTMinute){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	34 #converting the retention times (seconds) into minutes
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	35 print("converting the retention times into minutes in the variableMetadata")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	36 variableMetadata[,"rt"] <- variableMetadata[,"rt"]/60
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	37 variableMetadata[,"rtmin"] <- variableMetadata[,"rtmin"]/60
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	38 variableMetadata[,"rtmax"] <- variableMetadata[,"rtmax"]/60
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	39 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	40 return (variableMetadata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	41 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	42
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	43 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	44 # This function format ions identifiers
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	45 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	46 splitDeco <- strsplit(as.character(variableMetadata$name),"_")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	47 idsDeco <- sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	48 namecustom <- make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	49 variableMetadata <- cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	50 return(variableMetadata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	51 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	52
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	53 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	54 # Draw the plotChromPeakDensity 3 per page in a pdf file
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	55 getPlotChromPeakDensity <- function(xdata, mzdigit=4) {
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	56 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	57
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	58 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	59
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	60 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	61 names(group_colors) <- unique(xdata$sample_group)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	62
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	63 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	64 for (i in 1:nrow(featureDefinitions(xdata))) {
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	65 mzmin = featureDefinitions(xdata)[i,]$mzmin
17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	66 mzmax = featureDefinitions(xdata)[i,]$mzmax
17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	67 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	68 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	69 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	70
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	71 dev.off()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	72 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	73
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	74 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	75 # Draw the plotChromPeakDensity 3 per page in a pdf file
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	76 getPlotAdjustedRtime <- function(xdata) {
31 0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	77
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	78 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
31 0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	79
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	80 # Color by group
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	81 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	82 names(group_colors) <- unique(xdata$sample_group)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	83 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	84 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
31 0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	85
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	86 # Color by sample
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	87 plotAdjustedRtime(xdata, col = rainbow(length(xdata@phenoData@data$sample_name)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	88 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
31 0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	89
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	90 dev.off()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	91 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	92
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	93 #@author G. Le Corguille
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	94 # value: intensity values to be used into, maxo or intb
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	95 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, variableMetadataOutput, dataMatrixOutput) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	96 dataMatrix <- featureValues(xdata, method="medret", value=intval)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	97 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	98 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	99 variableMetadata <- featureDefinitions(xdata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	100 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	101 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	102
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	103 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	104 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	105
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	106 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	107 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	108
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	109 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	110
31 0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	111 #@author G. Le Corguille
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	112 getPlotChromatogram <- function(xdata, pdfname="Chromatogram.pdf", aggregationFun = "max") {
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	113
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	114 chrom <- chromatogram(xdata, aggregationFun = aggregationFun)
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	115 if (aggregationFun == "sum")
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	116 type="Total Ion Chromatograms"
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	117 else
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	118 type="Base Peak Intensity Chromatograms"
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	119
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	120 adjusted="Raw"
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	121 if (hasAdjustedRtime(xdata))
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	122 adjusted="Adjusted"
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	123
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	124 main <- paste(type,":",adjusted,"data")
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	125
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	126 pdf(pdfname, width=16, height=10)
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	127
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	128 # Color by group
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	129 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	130 names(group_colors) <- unique(xdata$sample_group)
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	131 plot(chrom, col = group_colors[chrom$sample_group], main=main)
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	132 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	133
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	134 # Color by sample
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	135 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main)
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	136 legend("topright", legend=xdata@phenoData@data$sample_name, col=rainbow(length(xdata@phenoData@data$sample_name)), cex=0.8, lty=1)
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	137
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	138 dev.off()
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	139 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	140
31 0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	141 #@author G. Le Corguille
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	142 getPlotTICs <- function(xdata, pdfname="TICs.pdf") {
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	143 getPlotChromatogram(xdata, pdfname, aggregationFun = "sum")
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	144 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	145
31 0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	146 #@author G. Le Corguille
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	147 getPlotBPIs <- function(xdata, pdfname="BPIs.pdf") {
0b5521b78c92 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309 lecorguille parents: 30 diff changeset	148 getPlotChromatogram(xdata, pdfname, aggregationFun = "max")
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	149 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	150
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	151
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	152 # Get the polarities from all the samples of a condition
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	153 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	154 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	155 getSampleMetadata <- function(xdata=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	156 cat("Creating the sampleMetadata file...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	157
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	158 #Create the sampleMetada dataframe
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	159 sampleMetadata <- xdata@phenoData@data
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	160 rownames(sampleMetadata) <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	161 colnames(sampleMetadata) <- c("sampleMetadata", "class")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	162
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	163 sampleNamesOrigin <- sampleMetadata$sampleMetadata
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	164 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	165
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	166 if (any(duplicated(sampleNamesMakeNames))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	167 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	168 for (sampleName in sampleNamesOrigin) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	169 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	170 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	171 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	172 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	173
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	174 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	175 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	176 for (sampleName in sampleNamesOrigin) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	177 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	178 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	179 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	180
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	181 sampleMetadata$sampleMetadata <- sampleNamesMakeNames
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	182
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	183
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	184 #For each sample file, the following actions are done
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	185 for (fileIdx in 1:length(fileNames(xdata))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	186 #Check if the file is in the CDF format
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	187 if (!mzR:::netCDFIsFile(fileNames(xdata))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	188
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	189 # If the column isn't exist, with add one filled with NA
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	190 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity <- NA
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	191
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	192 #Extract the polarity (a list of polarities)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	193 polarity <- fData(xdata)[fData(xdata)$fileIdx == fileIdx,"polarity"]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	194 #Verify if all the scans have the same polarity
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	195 uniq_list <- unique(polarity)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	196 if (length(uniq_list)>1){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	197 polarity <- "mixed"
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	198 } else {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	199 polarity <- as.character(uniq_list)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	200 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	201
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	202 #Set the polarity attribute
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	203 sampleMetadata$polarity[fileIdx] <- polarity
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	204 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	205
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	206 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	207
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	208 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	209
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	210 return(list("sampleNamesOrigin"=sampleNamesOrigin, "sampleNamesMakeNames"=sampleNamesMakeNames))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	211
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	212 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	213
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	214
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	215 # This function check if xcms will found all the files
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	216 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	217 checkFilesCompatibilityWithXcms <- function(directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	218 cat("Checking files filenames compatibilities with xmcs...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	219 # WHAT XCMS WILL FIND
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	220 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	221 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	222 info <- file.info(directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	223 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	224 files <- c(directory[!info$isdir], listed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	225 files_abs <- file.path(getwd(), files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	226 exists <- file.exists(files_abs)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	227 files[exists] <- files_abs[exists]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	228 files[exists] <- sub("//","/",files[exists])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	229
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	230 # WHAT IS ON THE FILESYSTEM
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	231 filesystem_filepaths <- system(paste0("find \"$PWD/",directory,"\" -not -name '\\.' -not -path 'conda-env' -type f -name \"\""), intern=T)
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	232 filesystem_filepaths <- filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	233
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	234 # COMPARISON
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	235 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	236 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	237 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	238 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	239 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	240 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	241
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	242
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	243 #This function list the compatible files within the directory as xcms did
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	244 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	245 getMSFiles <- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	246 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	247 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	248 info <- file.info(directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	249 listed <- list.files(directory[info$isdir], pattern=filepattern,recursive=TRUE, full.names=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	250 files <- c(directory[!info$isdir], listed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	251 exists <- file.exists(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	252 files <- files[exists]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	253 return(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	254 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	255
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	256 # This function check if XML contains special caracters. It also checks integrity and completness.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	257 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	258 checkXmlStructure <- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	259 cat("Checking XML structure...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	260
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	261 cmd <- paste0("IFS=$'\n'; for xml in $(find '",directory,"' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	262 capture <- system(cmd, intern=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	263
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	264 if (length(capture)>0){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	265 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	266 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	267 write(capture, stderr())
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	268 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	269 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	270
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	271 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	272
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	273
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	274 # This function check if XML contain special characters
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	275 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	276 deleteXmlBadCharacters<- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	277 cat("Checking Non ASCII characters in the XML...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	278
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	279 processed <- F
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	280 l <- system( paste0("find '",directory, "' -not -name '\\.' -not -path 'conda-env' -type f -iname '.ml'"), intern=TRUE)
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	281 for (i in l){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	282 cmd <- paste("LC_ALL=C grep '[^ -~]' \"", i, "\"", sep="")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	283 capture <- suppressWarnings(system(cmd, intern=TRUE))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	284 if (length(capture)>0){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	285 cmd <- paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	286 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	287 c <- system(cmd, intern=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	288 capture <- ""
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	289 processed <- T
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	290 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	291 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	292 if (processed) cat("\n\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	293 return(processed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	294 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	295
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	296
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	297 # This function will compute MD5 checksum to check the data integrity
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	298 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	299 getMd5sum <- function (directory) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	300 cat("Compute md5 checksum...\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	301 # WHAT XCMS WILL FIND
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	302 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	303 filepattern <- paste(paste("\\.", filepattern, "$", sep=""),collapse="\|")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	304 info <- file.info(directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	305 listed <- list.files(directory[info$isdir], pattern=filepattern, recursive=TRUE, full.names=TRUE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	306 files <- c(directory[!info$isdir], listed)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	307 exists <- file.exists(files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	308 files <- files[exists]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	309
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	310 library(tools)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	311
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	312 #cat("\n\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	313
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	314 return(as.matrix(md5sum(files)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	315 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	316
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	317
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	318 # This function get the raw file path from the arguments
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	319 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	320 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	321 if (!is.null(args$zipfile)) zipfile <- args$zipfile
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	322 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	323 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	324
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	325 if (!is.null(args$singlefile_galaxyPath)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	326 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	327 singlefile_sampleNames <- args$singlefile_sampleName
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	328 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	329 if (!is.null(args$singlefile_galaxyPathPositive)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	330 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	331 singlefile_sampleNames <- args$singlefile_sampleNamePositive
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	332 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	333 if (!is.null(args$singlefile_galaxyPathNegative)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	334 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	335 singlefile_sampleNames <- args$singlefile_sampleNameNegative
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	336 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	337 if (exists("singlefile_galaxyPaths")){
30 17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	338 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths,"\\\|"))
17562a6799a1 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7b226c3ba91a3cf654ec1c14b3ef85090968bb0f lecorguille parents: 29 diff changeset	339 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames,"\\\|"))
29 3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	340
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	341 singlefile <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	342 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	343 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	344 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	345 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	346 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	347 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	348 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	349 args[[argument]] <- NULL
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	350 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	351 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	352 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	353
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	354
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	355 # This function retrieve the raw file in the working directory
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	356 # - if zipfile: unzip the file with its directory tree
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	357 # - if singlefiles: set symlink with the good filename
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	358 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	359 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	360 if(!is.null(singlefile) && (length("singlefile")>0)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	361 for (singlefile_sampleName in names(singlefile)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	362 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	363 if(!file.exists(singlefile_galaxyPath)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	364 error_message <- paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	365 print(error_message); stop(error_message)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	366 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	367
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	368 if (!suppressWarnings( try (file.link(singlefile_galaxyPath, singlefile_sampleName), silent=T)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	369 file.copy(singlefile_galaxyPath, singlefile_sampleName)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	370
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	371 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	372 directory <- "."
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	373
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	374 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	375 if(!is.null(zipfile) && (zipfile != "")) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	376 if(!file.exists(zipfile)){
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	377 error_message <- paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	378 print(error_message)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	379 stop(error_message)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	380 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	381
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	382 #list all file in the zip file
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	383 #zip_files <- unzip(zipfile,list=T)[,"Name"]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	384
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	385 #unzip
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	386 suppressWarnings(unzip(zipfile, unzip="unzip"))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	387
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	388 #get the directory name
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	389 suppressWarnings(filesInZip <- unzip(zipfile, list=T))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	390 directories <- unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	391 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	392 directory <- "."
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	393 if (length(directories) == 1) directory <- directories
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	394
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	395 cat("files_root_directory\t",directory,"\n")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	396
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	397 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	398 return (directory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	399 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	400
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	401
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	402 # This function retrieve a xset like object
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	403 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	404 getxcmsSetObject <- function(xobject) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	405 # XCMS 1.x
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	406 if (class(xobject) == "xcmsSet")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	407 return (xobject)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	408 # XCMS 3.x
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	409 if (class(xobject) == "XCMSnExp") {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	410 # Get the legacy xcmsSet object
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	411 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	412 sampclass(xset) <- xset@phenoData$sample_group
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	413 return (xset)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	414 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	415 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	416
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	417
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	418 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	419 # https://github.com/sneumann/xcms/issues/250
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	420 groupnamesW4M <- function(xdata, mzdec = 0, rtdec = 0) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	421 mzfmt <- paste("%.", mzdec, "f", sep = "")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	422 rtfmt <- paste("%.", rtdec, "f", sep = "")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	423
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	424 gnames <- paste("M", sprintf(mzfmt, featureDefinitions(xdata)[,"mzmed"]), "T",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	425 sprintf(rtfmt, featureDefinitions(xdata)[,"rtmed"]), sep = "")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	426
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	427 if (any(dup <- duplicated(gnames)))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	428 for (dupname in unique(gnames[dup])) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	429 dupidx <- which(gnames == dupname)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	430 gnames[dupidx] <- paste(gnames[dupidx], seq(along = dupidx), sep = "_")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	431 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	432
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	433 return (gnames)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	434 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	435
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	436 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	437 # https://github.com/sneumann/xcms/issues/247
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	438 .concatenate_XCMSnExp <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	439 x <- list(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	440 if (length(x) == 0)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	441 return(NULL)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	442 if (length(x) == 1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	443 return(x[[1]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	444 ## Check that all are XCMSnExp objects.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	445 if (!all(unlist(lapply(x, function(z) is(z, "XCMSnExp")))))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	446 stop("All passed objects should be 'XCMSnExp' objects")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	447 new_x <- as(.concatenate_OnDiskMSnExp(...), "XCMSnExp")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	448 ## If any of the XCMSnExp has alignment results or detected features drop
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	449 ## them!
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	450 x <- lapply(x, function(z) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	451 if (hasAdjustedRtime(z)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	452 z <- dropAdjustedRtime(z)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	453 warning("Adjusted retention times found, had to drop them.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	454 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	455 if (hasFeatures(z)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	456 z <- dropFeatureDefinitions(z)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	457 warning("Feature definitions found, had to drop them.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	458 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	459 z
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	460 })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	461 ## Combine peaks
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	462 fls <- lapply(x, fileNames)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	463 startidx <- cumsum(lengths(fls))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	464 pks <- lapply(x, chromPeaks)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	465 procH <- lapply(x, processHistory)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	466 for (i in 2:length(fls)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	467 pks[[i]][, "sample"] <- pks[[i]][, "sample"] + startidx[i - 1]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	468 procH[[i]] <- lapply(procH[[i]], function(z) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	469 z@fileIndex <- as.integer(z@fileIndex + startidx[i - 1])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	470 z
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	471 })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	472 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	473 pks <- do.call(rbind, pks)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	474 new_x@.processHistory <- unlist(procH)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	475 chromPeaks(new_x) <- pks
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	476 if (validObject(new_x))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	477 new_x
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	478 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	479
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	480 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	481 # https://github.com/sneumann/xcms/issues/247
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	482 .concatenate_OnDiskMSnExp <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	483 x <- list(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	484 if (length(x) == 0)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	485 return(NULL)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	486 if (length(x) == 1)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	487 return(x[[1]])
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	488 ## Check that all are XCMSnExp objects.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	489 if (!all(unlist(lapply(x, function(z) is(z, "OnDiskMSnExp")))))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	490 stop("All passed objects should be 'OnDiskMSnExp' objects")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	491 ## Check processingQueue
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	492 procQ <- lapply(x, function(z) z@spectraProcessingQueue)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	493 new_procQ <- procQ[[1]]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	494 is_ok <- unlist(lapply(procQ, function(z)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	495 !is.character(all.equal(new_procQ, z))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	496 ))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	497 if (any(!is_ok)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	498 warning("Processing queues from the submitted objects differ! ",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	499 "Dropping the processing queue.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	500 new_procQ <- list()
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	501 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	502 ## processingData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	503 fls <- lapply(x, function(z) z@processingData@files)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	504 startidx <- cumsum(lengths(fls))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	505 ## featureData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	506 featd <- lapply(x, fData)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	507 ## Have to update the file index and the spectrum names.
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	508 for (i in 2:length(featd)) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	509 featd[[i]]$fileIdx <- featd[[i]]$fileIdx + startidx[i - 1]
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	510 rownames(featd[[i]]) <- MSnbase:::formatFileSpectrumNames(
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	511 fileIds = featd[[i]]$fileIdx,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	512 spectrumIds = featd[[i]]$spIdx,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	513 nSpectra = nrow(featd[[i]]),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	514 nFiles = length(unlist(fls))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	515 )
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	516 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	517 featd <- do.call(rbind, featd)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	518 featd$spectrum <- 1:nrow(featd)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	519 ## experimentData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	520 expdata <- lapply(x, function(z) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	521 ed <- z@experimentData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	522 data.frame(instrumentManufacturer = ed@instrumentManufacturer,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	523 instrumentModel = ed@instrumentModel,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	524 ionSource = ed@ionSource,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	525 analyser = ed@analyser,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	526 detectorType = ed@detectorType,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	527 stringsAsFactors = FALSE)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	528 })
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	529 expdata <- do.call(rbind, expdata)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	530 expdata <- new("MIAPE",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	531 instrumentManufacturer = expdata$instrumentManufacturer,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	532 instrumentModel = expdata$instrumentModel,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	533 ionSource = expdata$ionSource,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	534 analyser = expdata$analyser,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	535 detectorType = expdata$detectorType)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	536
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	537 ## protocolData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	538 protodata <- lapply(x, function(z) z@protocolData)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	539 if (any(unlist(lapply(protodata, nrow)) > 0))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	540 warning("Found non-empty protocol data, but merging protocol data is",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	541 " currently not supported. Skipped.")
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	542 ## phenoData
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	543 pdata <- do.call(rbind, lapply(x, pData))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	544 res <- new(
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	545 "OnDiskMSnExp",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	546 phenoData = new("NAnnotatedDataFrame", data = pdata),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	547 featureData = new("AnnotatedDataFrame", featd),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	548 processingData = new("MSnProcess",
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	549 processing = paste0("Concatenated [", date(), "]"),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	550 files = unlist(fls), smoothed = NA),
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	551 experimentData = expdata,
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	552 spectraProcessingQueue = new_procQ)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	553 if (validObject(res))
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	554 res
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	555 }
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	556
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	557 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	558 # https://github.com/sneumann/xcms/issues/247
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	559 c.XCMSnExp <- function(...) {
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	560 .concatenate_XCMSnExp(...)
3d4339594010 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e384d6dd5f410799ec211f73bca0b5d5d7bc651e lecorguille parents: diff changeset	561 }

Mercurial > repos > lecorguille > xcms_summary

annotate lib.r @ 31:0b5521b78c92 draft