diff lib.r @ 18:8e740205c907 draft

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

--- a/lib.r	Wed Feb 08 04:36:13 2017 -0500
+++ b/lib.r	Wed Feb 08 05:27:04 2017 -0500
@@ -27,28 +27,32 @@
 
 #@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)
+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) {
-    variableMetadata_dataMatrix = peakTable(xset, method="medret", value=intval)
-    variableMetadata_dataMatrix = cbind(name=groupnames(xset),variableMetadata_dataMatrix)
+    groups <- xset@groups
+    values <- groupval(xset, "medret", value=intval)
 
-    dataMatrix = variableMetadata_dataMatrix[,(make.names(colnames(variableMetadata_dataMatrix)) %in% c("name", make.names(sampnames(xset))))]
+    # 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)
 
-    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)
+    rownames(groups) = ids
+    rownames(values) = ids
 
-    write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
-    write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
+    #@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