diff lib.r @ 16:6a4d8753a330 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 10:37:03 -0400
parents 833d2c821d9c
children 7a19925478e8
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line diff
--- a/lib.r	Wed Sep 19 02:53:56 2018 -0400
+++ b/lib.r	Thu Oct 04 10:37:03 2018 -0400
@@ -186,9 +186,9 @@
 
 #@author G. Le Corguille
 # value: intensity values to be used into, maxo or intb
-getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput) {
+getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
     dataMatrix <- featureValues(xdata, method="medret", value=intval)
-    colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix))
+    colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
     dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
     variableMetadata <- featureDefinitions(xdata)
     colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"