Mercurial > repos > lecorguille > xcms_merge

comparison lib.r @ 5:7bb43bf0b546 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e3956bf3393be5bff67b4d90f1007da00b0ec9b2-dirty
author lecorguille
date Thu, 04 Oct 2018 10:36:22 -0400
parents f439ed7a8f03
children a9d451591d7b
comparison
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4:4c25647cd4df 5:7bb43bf0b546
184 dev.off() 184 dev.off()
185 } 185 }
186 186
187 #@author G. Le Corguille 187 #@author G. Le Corguille
188 # value: intensity values to be used into, maxo or intb 188 # value: intensity values to be used into, maxo or intb
189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput) { 189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
190 dataMatrix <- featureValues(xdata, method="medret", value=intval) 190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
191 colnames(dataMatrix) <- tools::file_path_sans_ext(colnames(dataMatrix)) 191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
192 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix) 192 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix)
193 variableMetadata <- featureDefinitions(xdata) 193 variableMetadata <- featureDefinitions(xdata)
194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" 194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) 195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata)
196 196