Mercurial > repos > lecorguille > xcms_xcmsset

comparison lib.r @ 20:41cf6f56d1b6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
author lecorguille
date Fri, 09 Nov 2018 15:10:13 -0500
parents 517d4375db53
children 87df3692c68d
comparison
equal deleted inserted replaced
19:57fcba888b00 20:41cf6f56d1b6
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)
200 200
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 = ",")
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 }
205 208
258 cat("Creating the sampleMetadata file...\n") 261 cat("Creating the sampleMetadata file...\n")
259 262
260 #Create the sampleMetada dataframe 263 #Create the sampleMetada dataframe
261 sampleMetadata <- xdata@phenoData@data 264 sampleMetadata <- xdata@phenoData@data
262 rownames(sampleMetadata) <- NULL 265 rownames(sampleMetadata) <- NULL
263 colnames(sampleMetadata) <- c("sampleMetadata", "class") 266 colnames(sampleMetadata) <- c("sample_name", "class")
264 267
265 sampleNamesOrigin <- sampleMetadata$sampleMetadata 268 sampleNamesOrigin <- sampleMetadata$sample_name
266 sampleNamesMakeNames <- make.names(sampleNamesOrigin) 269 sampleNamesMakeNames <- make.names(sampleNamesOrigin)
267 270
268 if (any(duplicated(sampleNamesMakeNames))) { 271 if (any(duplicated(sampleNamesMakeNames))) {
269 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()) 272 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())
270 for (sampleName in sampleNamesOrigin) { 273 for (sampleName in sampleNamesOrigin) {
278 for (sampleName in sampleNamesOrigin) { 281 for (sampleName in sampleNamesOrigin) {
279 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) 282 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
280 } 283 }
281 } 284 }
282 285
283 sampleMetadata$sampleMetadata <- sampleNamesMakeNames 286 sampleMetadata$sample_name <- sampleNamesMakeNames
284 287
285 288
286 #For each sample file, the following actions are done 289 #For each sample file, the following actions are done
287 for (fileIdx in 1:length(fileNames(xdata))) { 290 for (fileIdx in 1:length(fileNames(xdata))) {
288 #Check if the file is in the CDF format 291 #Check if the file is in the CDF format