Mercurial > repos > lecorguille > xcms_retcor
annotate lib.r @ 7:bb602a5b8819 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
author | lecorguille |
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date | Mon, 30 Jan 2017 08:53:30 -0500 |
parents | 54cc3edfe35c |
children | 4bfef820569b |
rev | line source |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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1 #Authors ABiMS TEAM |
7
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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2 #Lib.r for Galaxy Workflow4Metabolomics xcms tools |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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3 # |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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4 #version 2.4: lecorguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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5 # add getPeaklistW4M |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
changeset
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6 #version 2.3: yguitton |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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7 # correction for empty PDF when only 1 class |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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changeset
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8 #version 2.2 |
7
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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9 # correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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10 # Note if scanrange is used a warning is prompted in R console but do not stop PDF generation |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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11 #version 2.1: yguitton |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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12 # Modifications made by Guitton Yann |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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13 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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14 |
7
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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15 #@author G. Le Corguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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16 #This function convert if it is required the Retention Time in minutes |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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17 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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18 if (convertRTMinute){ |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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19 #converting the retention times (seconds) into minutes |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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20 print("converting the retention times into minutes in the variableMetadata") |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
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21 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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22 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
changeset
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23 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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24 } |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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25 return (variableMetadata) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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26 } |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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changeset
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27 |
7
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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28 #@author G. Le Corguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
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29 #This function format ions identifiers |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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30 formatIonIdentifiers <- function(dataData, numDigitsRT=0, numDigitsMZ=0) { |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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31 return(make.unique(paste0("M",round(dataData[,"mz"],numDigitsMZ),"T",round(dataData[,"rt"],numDigitsRT)))) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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32 } |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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33 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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34 #@author G. Le Corguille |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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35 # value: intensity values to be used into, maxo or intb |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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36 getPeaklistW4M <- function(xset, intval="into",convertRTMinute=F,numDigitsMZ=4,numDigitsRT=0,variableMetadataOutput,dataMatrixOutput) { |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
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37 groups <- xset@groups |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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38 values <- groupval(xset, "medret", value=intval) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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39 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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40 # renamming of the column rtmed to rt to fit with camera peaklist function output |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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41 colnames(groups)[colnames(groups)=="rtmed"] <- "rt" |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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42 colnames(groups)[colnames(groups)=="mzmed"] <- "mz" |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
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43 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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44 ids <- formatIonIdentifiers(groups, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
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45 groups = RTSecondToMinute(groups, convertRTMinute) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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46 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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47 rownames(groups) = ids |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
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48 rownames(values) = ids |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
2
diff
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49 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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50 #@TODO: add "name" as the first column name |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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51 #colnames(groups)[1] = "name" |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
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52 #colnames(values)[1] = "name" |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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53 |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
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54 write.table(groups, file=variableMetadataOutput,sep="\t",quote=F,row.names = T,col.names = NA) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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diff
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55 write.table(values, file=dataMatrixOutput,sep="\t",quote=F,row.names = T,col.names = NA) |
bb602a5b8819
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents:
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56 } |
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54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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57 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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58 #@author Y. Guitton |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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59 getBPC <- function(file,rtcor=NULL, ...) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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60 object <- xcmsRaw(file) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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61 sel <- profRange(object, ...) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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62 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE])) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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63 #plotChrom(xcmsRaw(file), base=T) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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64 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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65 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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66 #@author Y. Guitton |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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67 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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68 cat("Creating BIC pdf...\n") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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69 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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70 if (is.null(xcmsSet)) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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71 cat("Enter an xcmsSet \n") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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72 stop() |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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73 } else { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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74 files <- filepaths(xcmsSet) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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75 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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76 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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77 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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78 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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79 classnames<-vector("list",length(class)) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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80 for (i in 1:length(class)){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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81 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i]) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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82 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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83 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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84 N <- dim(phenoData(xcmsSet))[1] |
54cc3edfe35c
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85 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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86 TIC <- vector("list",N) |
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87 |
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88 |
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89 for (j in 1:N) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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90 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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91 TIC[[j]] <- getBPC(files[j]) |
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92 #good for raw |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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93 # seems strange for corrected |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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94 #errors if scanrange used in xcmsSetgeneration |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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95 if (!is.null(xcmsSet) && rt == "corrected") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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96 rtcor <- xcmsSet@rt$corrected[[j]] else |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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97 rtcor <- NULL |
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98 |
2
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99 TIC[[j]] <- getBPC(files[j],rtcor=rtcor) |
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100 # TIC[[j]][,1]<-rtcor |
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101 } |
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102 |
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103 |
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104 |
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105 pdf(pdfname,w=16,h=10) |
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106 cols <- rainbow(N) |
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107 lty = 1:N |
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108 pch = 1:N |
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109 #search for max x and max y in BPCs |
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110 xlim = range(sapply(TIC, function(x) range(x[,1]))) |
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111 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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112 ylim = c(-ylim[2], ylim[2]) |
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113 |
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114 |
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115 ##plot start |
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116 |
2
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117 if (length(class)>2){ |
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118 for (k in 1:(length(class)-1)){ |
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119 for (l in (k+1):length(class)){ |
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120 #print(paste(class[k],"vs",class[l],sep=" ")) |
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121 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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122 colvect<-NULL |
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123 for (j in 1:length(classnames[[k]])) { |
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124 tic <- TIC[[classnames[[k]][j]]] |
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125 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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126 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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127 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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128 } |
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129 for (j in 1:length(classnames[[l]])) { |
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130 # i=class2names[j] |
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131 tic <- TIC[[classnames[[l]][j]]] |
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132 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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133 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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134 } |
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135 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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136 } |
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137 } |
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138 }#end if length >2 |
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139 |
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140 if (length(class)==2){ |
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141 k=1 |
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142 l=2 |
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143 colvect<-NULL |
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144 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC") |
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145 |
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146 for (j in 1:length(classnames[[k]])) { |
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147 |
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148 tic <- TIC[[classnames[[k]][j]]] |
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149 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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150 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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151 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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152 } |
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153 for (j in 1:length(classnames[[l]])) { |
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154 # i=class2names[j] |
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155 tic <- TIC[[classnames[[l]][j]]] |
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156 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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157 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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158 } |
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159 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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160 |
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161 }#end length ==2 |
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162 |
7
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163 #case where only one class |
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164 if (length(class)==1){ |
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165 k=1 |
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166 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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167 colvect<-NULL |
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168 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC") |
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169 |
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170 for (j in 1:length(classnames[[k]])) { |
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171 tic <- TIC[[classnames[[k]][j]]] |
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172 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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173 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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174 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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175 } |
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176 |
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177 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) |
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178 |
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179 }#end length ==1 |
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180 |
2
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181 dev.off() #pdf(pdfname,w=16,h=10) |
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182 |
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183 invisible(TIC) |
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184 } |
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185 |
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186 |
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187 |
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188 #@author Y. Guitton |
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189 getTIC <- function(file,rtcor=NULL) { |
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190 object <- xcmsRaw(file) |
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191 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity) |
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192 } |
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193 |
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194 ## |
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195 ## overlay TIC from all files in current folder or from xcmsSet, create pdf |
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196 ## |
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197 #@author Y. Guitton |
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198 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) { |
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199 cat("Creating TIC pdf...\n") |
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200 |
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201 if (is.null(xcmsSet)) { |
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202 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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203 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|") |
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204 if (is.null(files)) |
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205 files <- getwd() |
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206 info <- file.info(files) |
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207 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE) |
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208 files <- c(files[!info$isdir], listed) |
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209 } else { |
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210 files <- filepaths(xcmsSet) |
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211 } |
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212 |
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213 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class |
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214 |
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215 classnames<-vector("list",length(class)) |
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216 for (i in 1:length(class)){ |
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217 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i]) |
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218 } |
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219 |
2
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220 N <- length(files) |
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221 TIC <- vector("list",N) |
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222 |
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223 for (i in 1:N) { |
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224 if (!is.null(xcmsSet) && rt == "corrected") |
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225 rtcor <- xcmsSet@rt$corrected[[i]] else |
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226 rtcor <- NULL |
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227 TIC[[i]] <- getTIC(files[i],rtcor=rtcor) |
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228 } |
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229 |
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230 pdf(pdfname,w=16,h=10) |
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231 cols <- rainbow(N) |
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232 lty = 1:N |
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233 pch = 1:N |
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234 #search for max x and max y in TICs |
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235 xlim = range(sapply(TIC, function(x) range(x[,1]))) |
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236 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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237 ylim = c(-ylim[2], ylim[2]) |
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238 |
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239 |
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240 ##plot start |
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241 if (length(class)>2){ |
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242 for (k in 1:(length(class)-1)){ |
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243 for (l in (k+1):length(class)){ |
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244 #print(paste(class[k],"vs",class[l],sep=" ")) |
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245 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC") |
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246 colvect<-NULL |
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247 for (j in 1:length(classnames[[k]])) { |
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248 |
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249 tic <- TIC[[classnames[[k]][j]]] |
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250 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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251 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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252 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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253 } |
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254 for (j in 1:length(classnames[[l]])) { |
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255 # i=class2names[j] |
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256 tic <- TIC[[classnames[[l]][j]]] |
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257 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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258 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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259 } |
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260 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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261 } |
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262 } |
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263 }#end if length >2 |
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264 if (length(class)==2){ |
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265 k=1 |
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266 l=2 |
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267 |
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268 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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269 colvect<-NULL |
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270 for (j in 1:length(classnames[[k]])) { |
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271 tic <- TIC[[classnames[[k]][j]]] |
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272 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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273 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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274 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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275 } |
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276 for (j in 1:length(classnames[[l]])) { |
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277 # i=class2names[j] |
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278 tic <- TIC[[classnames[[l]][j]]] |
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279 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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280 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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281 } |
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282 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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283 |
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284 }#end length ==2 |
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285 |
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286 #case where only one class |
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287 if (length(class)==1){ |
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288 k=1 |
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289 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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290 |
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291 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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292 colvect<-NULL |
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293 for (j in 1:length(classnames[[k]])) { |
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294 tic <- TIC[[classnames[[k]][j]]] |
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295 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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296 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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297 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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298 } |
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299 |
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300 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch) |
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301 |
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302 }#end length ==1 |
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303 |
2
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304 dev.off() #pdf(pdfname,w=16,h=10) |
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305 |
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306 invisible(TIC) |
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307 } |
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308 |
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309 |
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310 |
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311 ## |
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312 ## Get the polarities from all the samples of a condition |
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313 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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314 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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315 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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316 cat("Creating the sampleMetadata file...\n") |
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317 |
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318 #Create the sampleMetada dataframe |
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319 sampleMetadata=xset@phenoData |
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320 sampleNamesOrigin=rownames(sampleMetadata) |
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321 sampleNamesMakeNames=make.names(sampleNamesOrigin) |
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322 |
2
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323 if (any(duplicated(sampleNamesMakeNames))) { |
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324 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()) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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325 for (sampleName in sampleNamesOrigin) { |
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326 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
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327 } |
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328 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
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329 } |
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330 |
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331 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
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332 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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333 for (sampleName in sampleNamesOrigin) { |
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334 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
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335 } |
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336 } |
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337 |
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338 sampleMetadata$sampleMetadata=sampleNamesMakeNames |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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339 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns |
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340 rownames(sampleMetadata)=NULL |
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341 |
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342 #Create a list of files name in the current directory |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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343 list_files=xset@filepaths |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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344 #For each sample file, the following actions are done |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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345 for (file in list_files){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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346 #Check if the file is in the CDF format |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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347 if (!mzR:::netCDFIsFile(file)){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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348 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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349 # If the column isn't exist, with add one filled with NA |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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350 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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351 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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352 #Create a simple xcmsRaw object for each sample |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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353 xcmsRaw=xcmsRaw(file) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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354 #Extract the polarity (a list of polarities) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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355 polarity=xcmsRaw@polarity |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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356 #Verify if all the scans have the same polarity |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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357 uniq_list=unique(polarity) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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358 if (length(uniq_list)>1){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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359 polarity="mixed" |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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360 } else { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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361 polarity=as.character(uniq_list) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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362 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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363 #Transforms the character to obtain only the sample name |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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364 filename=basename(file) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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365 library(tools) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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366 samplename=file_path_sans_ext(filename) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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367 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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368 #Set the polarity attribute |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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369 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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370 |
2
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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371 #Delete xcmsRaw object because it creates a bug for the fillpeaks step |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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372 rm(xcmsRaw) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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373 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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374 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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375 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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376 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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377 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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378 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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379 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames)) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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380 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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381 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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382 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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383 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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384 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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385 ## This function check if xcms will found all the files |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
386 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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387 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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388 checkFilesCompatibilityWithXcms <- function(directory) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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389 cat("Checking files filenames compatibilities with xmcs...\n") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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390 # WHAT XCMS WILL FIND |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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391 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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392 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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393 info <- file.info(directory) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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394 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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395 files <- c(directory[!info$isdir], listed) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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396 files_abs <- file.path(getwd(), files) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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397 exists <- file.exists(files_abs) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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398 files[exists] <- files_abs[exists] |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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399 files[exists] <- sub("//","/",files[exists]) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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400 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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401 # WHAT IS ON THE FILESYSTEM |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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402 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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403 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
404 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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405 # COMPARISON |
7
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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2
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406 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { |
2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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407 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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408 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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409 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
410 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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411 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
412 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
413 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
414 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
415 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
416 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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417 ## This function check if XML contains special caracters. It also checks integrity and completness. |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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418 ## |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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419 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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420 checkXmlStructure <- function (directory) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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diff
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|
421 cat("Checking XML structure...\n") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
422 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
423 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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424 capture=system(cmd,intern=TRUE) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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425 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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426 if (length(capture)>0){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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427 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
428 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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|
429 write(capture, stderr()) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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diff
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|
430 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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431 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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432 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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433 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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434 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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435 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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436 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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437 ## This function check if XML contain special characters |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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438 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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439 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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440 deleteXmlBadCharacters<- function (directory) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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441 cat("Checking Non ASCII characters in the XML...\n") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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442 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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443 processed=F |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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444 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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445 for (i in l){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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446 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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447 capture=suppressWarnings(system(cmd,intern=TRUE)) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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448 if (length(capture)>0){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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449 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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450 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") ) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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451 c=system(cmd,intern=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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452 capture="" |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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453 processed=T |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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454 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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455 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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456 if (processed) cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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457 return(processed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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458 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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459 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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460 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
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461 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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462 ## This function will compute MD5 checksum to check the data integrity |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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463 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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464 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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465 getMd5sum <- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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466 cat("Compute md5 checksum...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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467 # WHAT XCMS WILL FIND |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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468 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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469 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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470 info <- file.info(directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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471 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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472 files <- c(directory[!info$isdir], listed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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473 exists <- file.exists(files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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474 files <- files[exists] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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475 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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476 library(tools) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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477 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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478 #cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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479 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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480 return(as.matrix(md5sum(files))) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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481 } |