Mercurial > repos > lecorguille > xcms_export_samplemetadata

comparison lib.r @ 3:10f7b1548200 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
author lecorguille
date Fri, 09 Nov 2018 15:20:18 -0500
parents e3c06320f884
children 8c62030a1136
comparison
equal deleted inserted replaced
2:942ffa3c38b8 3:10f7b1548200
195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) 195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
196 196
197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) 197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) 198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) 199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
200
201 # FIX: issue when the vector at peakidx is too long and is written in a new line during the export
202 variableMetadata[,"peakidx"] <- vapply(variableMetadata[,"peakidx"], FUN = paste, FUN.VALUE = character(1), collapse = ",")
200 203
201 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F) 204 write.table(variableMetadata, file=variableMetadataOutput,sep="\t",quote=F,row.names=F)
202 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F) 205 write.table(dataMatrix, file=dataMatrixOutput,sep="\t",quote=F,row.names=F)
203 206
204 } 207 }