comparison lib.r @ 19:7b74ec867ad2 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 717c02f887ce343ca55f862c8020aaf49f5581d8

18:65dc5e8b53f7

    return (variableMetadata)
}

#@author G. Le Corguille
#This function format ions identifiers
formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
    splitDeco = strsplit(as.character(variableMetadata$name),"_")
    idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
    namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
    variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
    return(variableMetadata)
}

#@author G. Le Corguille
# value: intensity values to be used into, maxo or intb
getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {
    variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval)
    variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix)

    dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))]

    variableMetadata = variableMetadata_dataMatrix[,!(make.names(colnames(variableMetadata_dataMatrix)) %in% c(make.names(sampnames(xset))))]
    variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
    variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)

    write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
    write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
}

#@author Y. Guitton
getBPC <- function(file,rtcor=NULL, ...) {
    object <- xcmsRaw(file)

19:7b74ec867ad2

    return (variableMetadata)
}

#@author G. Le Corguille
#This function format ions identifiers
formatIonIdentifiers <- function(dataData, numDigitsRT=0, numDigitsMZ=0) {
    return(make.unique(paste0("M",round(dataData[,"mz"],numDigitsMZ),"T",round(dataData[,"rt"],numDigitsRT))))
}

#@author G. Le Corguille
# value: intensity values to be used into, maxo or intb
getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) {
    groups <- xset@groups
    values <- groupval(xset, "medret", value=intval)

    # renamming of the column rtmed to rt to fit with camera peaklist function output
    colnames(groups)[colnames(groups)=="rtmed"] <- "rt"
    colnames(groups)[colnames(groups)=="mzmed"] <- "mz"

    ids <- formatIonIdentifiers(groups, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
    groups = RTSecondToMinute(groups, convertRTMinute)

    rownames(groups) = ids
    rownames(values) = ids

    #@TODO: add "name" as the first column name
    #colnames(groups)[1] = "name"
    #colnames(values)[1] = "name"

    write.table(groups, file=variableMetadataOutput,sep="\t",quote=F,row.names = T,col.names = NA)
    write.table(values, file=dataMatrixOutput,sep="\t",quote=F,row.names = T,col.names = NA)
}

#@author Y. Guitton
getBPC <- function(file,rtcor=NULL, ...) {
    object <- xcmsRaw(file)