Mercurial > repos > lecorguille > xcms_retcor
annotate lib.r @ 3:3b44991a8e05 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
author | lecorguille |
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date | Mon, 25 Apr 2016 11:14:51 -0400 |
parents | 54cc3edfe35c |
children | bb602a5b8819 |
rev | line source |
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2
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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1 # lib.r version="2.0.1" |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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2 #Authors ABiMS TEAM |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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3 #Lib.r for Galaxy Workflow4Metabo |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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4 #version 2.2 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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5 #Based on lib.r 2.1 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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6 #Modifications made by Guitton Yann |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
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7 #correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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8 #Note if scanrange is used a warning is prompted in R console but do not stop PDF generation |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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9 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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10 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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11 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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12 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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13 #@author Y. Guitton |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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14 getBPC <- function(file,rtcor=NULL, ...) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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15 object <- xcmsRaw(file) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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16 sel <- profRange(object, ...) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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17 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
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18 #plotChrom(xcmsRaw(file), base=T) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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19 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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20 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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21 #@author Y. Guitton |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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22 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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23 cat("Creating BIC pdf...\n") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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24 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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25 if (is.null(xcmsSet)) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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26 cat("Enter an xcmsSet \n") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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27 stop() |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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28 } else { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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29 files <- filepaths(xcmsSet) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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30 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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31 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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32 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
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33 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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34 classnames<-vector("list",length(class)) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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35 for (i in 1:length(class)){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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36 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i]) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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37 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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38 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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39 N <- dim(phenoData(xcmsSet))[1] |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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40 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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41 TIC <- vector("list",N) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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42 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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43 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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44 for (j in 1:N) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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45 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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46 TIC[[j]] <- getBPC(files[j]) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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47 #good for raw |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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48 # seems strange for corrected |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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49 #errors if scanrange used in xcmsSetgeneration |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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50 if (!is.null(xcmsSet) && rt == "corrected") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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51 rtcor <- xcmsSet@rt$corrected[[j]] else |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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52 rtcor <- NULL |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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53 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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54 TIC[[j]] <- getBPC(files[j],rtcor=rtcor) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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55 # TIC[[j]][,1]<-rtcor |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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56 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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57 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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58 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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59 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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60 pdf(pdfname,w=16,h=10) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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61 cols <- rainbow(N) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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62 lty = 1:N |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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63 pch = 1:N |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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64 #search for max x and max y in BPCs |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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65 xlim = range(sapply(TIC, function(x) range(x[,1]))) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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66 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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67 ylim = c(-ylim[2], ylim[2]) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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68 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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69 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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70 ##plot start |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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71 |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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72 if (length(class)>2){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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73 for (k in 1:(length(class)-1)){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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74 for (l in (k+1):length(class)){ |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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75 #print(paste(class[k],"vs",class[l],sep=" ")) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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76 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") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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77 colvect<-NULL |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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78 for (j in 1:length(classnames[[k]])) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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79 tic <- TIC[[classnames[[k]][j]]] |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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80 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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81 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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82 colvect<-append(colvect,cols[classnames[[k]][j]]) |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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83 } |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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84 for (j in 1:length(classnames[[l]])) { |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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85 # i=class2names[j] |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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86 tic <- TIC[[classnames[[l]][j]]] |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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87 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
54cc3edfe35c
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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88 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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89 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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90 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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91 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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92 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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93 }#end if length >2 |
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94 |
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95 if (length(class)==2){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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96 k=1 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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97 l=2 |
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98 colvect<-NULL |
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99 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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100 |
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101 for (j in 1:length(classnames[[k]])) { |
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102 |
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103 tic <- TIC[[classnames[[k]][j]]] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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104 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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105 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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106 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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107 } |
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108 for (j in 1:length(classnames[[l]])) { |
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109 # i=class2names[j] |
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110 tic <- TIC[[classnames[[l]][j]]] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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111 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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112 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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113 } |
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114 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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115 |
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116 }#end length ==2 |
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117 |
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118 dev.off() #pdf(pdfname,w=16,h=10) |
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119 |
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120 invisible(TIC) |
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121 } |
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122 |
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123 |
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124 |
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125 #@author Y. Guitton |
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126 getTIC <- function(file,rtcor=NULL) { |
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127 object <- xcmsRaw(file) |
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128 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity) |
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129 } |
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130 |
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131 ## |
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132 ## overlay TIC from all files in current folder or from xcmsSet, create pdf |
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133 ## |
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134 #@author Y. Guitton |
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135 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) { |
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136 cat("Creating TIC pdf...\n") |
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137 |
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138 if (is.null(xcmsSet)) { |
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139 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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140 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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141 if (is.null(files)) |
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142 files <- getwd() |
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143 info <- file.info(files) |
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144 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE) |
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145 files <- c(files[!info$isdir], listed) |
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146 } else { |
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147 files <- filepaths(xcmsSet) |
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148 } |
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149 |
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150 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class |
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151 |
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152 classnames<-vector("list",length(class)) |
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153 for (i in 1:length(class)){ |
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154 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i]) |
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155 } |
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156 |
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157 N <- length(files) |
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158 TIC <- vector("list",N) |
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159 |
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160 for (i in 1:N) { |
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161 if (!is.null(xcmsSet) && rt == "corrected") |
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162 rtcor <- xcmsSet@rt$corrected[[i]] else |
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163 rtcor <- NULL |
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164 TIC[[i]] <- getTIC(files[i],rtcor=rtcor) |
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165 } |
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166 |
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167 pdf(pdfname,w=16,h=10) |
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168 cols <- rainbow(N) |
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169 lty = 1:N |
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170 pch = 1:N |
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171 #search for max x and max y in TICs |
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172 xlim = range(sapply(TIC, function(x) range(x[,1]))) |
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173 ylim = range(sapply(TIC, function(x) range(x[,2]))) |
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174 ylim = c(-ylim[2], ylim[2]) |
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175 |
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176 |
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177 ##plot start |
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178 if (length(class)>2){ |
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179 for (k in 1:(length(class)-1)){ |
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180 for (l in (k+1):length(class)){ |
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181 #print(paste(class[k],"vs",class[l],sep=" ")) |
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182 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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183 colvect<-NULL |
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184 for (j in 1:length(classnames[[k]])) { |
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185 |
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186 tic <- TIC[[classnames[[k]][j]]] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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187 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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188 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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189 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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190 } |
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191 for (j in 1:length(classnames[[l]])) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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192 # i=class2names[j] |
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193 tic <- TIC[[classnames[[l]][j]]] |
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194 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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195 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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196 } |
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197 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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198 } |
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199 } |
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200 }#end if length >2 |
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201 if (length(class)==2){ |
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202 k=1 |
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203 l=2 |
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204 |
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205 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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206 colvect<-NULL |
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207 for (j in 1:length(classnames[[k]])) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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208 tic <- TIC[[classnames[[k]][j]]] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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209 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l") |
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210 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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211 colvect<-append(colvect,cols[classnames[[k]][j]]) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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212 } |
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213 for (j in 1:length(classnames[[l]])) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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214 # i=class2names[j] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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215 tic <- TIC[[classnames[[l]][j]]] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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216 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l") |
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217 colvect<-append(colvect,cols[classnames[[l]][j]]) |
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218 } |
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219 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) |
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220 |
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221 }#end length ==2 |
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222 dev.off() #pdf(pdfname,w=16,h=10) |
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223 |
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224 invisible(TIC) |
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225 } |
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226 |
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227 |
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228 |
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229 ## |
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230 ## Get the polarities from all the samples of a condition |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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231 #@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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232 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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233 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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234 cat("Creating the sampleMetadata file...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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235 |
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236 #Create the sampleMetada dataframe |
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237 sampleMetadata=xset@phenoData |
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238 sampleNamesOrigin=rownames(sampleMetadata) |
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239 sampleNamesMakeNames=make.names(sampleNamesOrigin) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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240 |
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241 if (any(duplicated(sampleNamesMakeNames))) { |
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242 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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243 for (sampleName in sampleNamesOrigin) { |
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244 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr()) |
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245 } |
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246 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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247 } |
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248 |
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249 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) { |
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250 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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251 for (sampleName in sampleNamesOrigin) { |
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252 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n")) |
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253 } |
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254 } |
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255 |
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256 sampleMetadata$sampleMetadata=sampleNamesMakeNames |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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257 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns |
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258 rownames(sampleMetadata)=NULL |
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259 |
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260 #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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261 list_files=xset@filepaths |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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262 #For each sample file, the following actions are done |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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263 for (file in list_files){ |
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264 #Check if the file is in the CDF format |
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265 if (!mzR:::netCDFIsFile(file)){ |
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266 |
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267 # If the column isn't exist, with add one filled with NA |
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268 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA |
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269 |
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270 #Create a simple xcmsRaw object for each sample |
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271 xcmsRaw=xcmsRaw(file) |
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272 #Extract the polarity (a list of polarities) |
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273 polarity=xcmsRaw@polarity |
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274 #Verify if all the scans have the same polarity |
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275 uniq_list=unique(polarity) |
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276 if (length(uniq_list)>1){ |
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277 polarity="mixed" |
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278 } else { |
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279 polarity=as.character(uniq_list) |
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280 } |
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281 #Transforms the character to obtain only the sample name |
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282 filename=basename(file) |
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283 library(tools) |
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284 samplename=file_path_sans_ext(filename) |
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285 |
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286 #Set the polarity attribute |
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287 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity |
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288 |
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289 #Delete xcmsRaw object because it creates a bug for the fillpeaks step |
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290 rm(xcmsRaw) |
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291 } |
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292 |
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293 } |
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294 |
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295 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput) |
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296 |
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297 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames)) |
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298 |
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299 } |
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300 |
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301 |
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302 ## |
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303 ## This function check if xcms will found all the files |
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304 ## |
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305 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM |
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306 checkFilesCompatibilityWithXcms <- function(directory) { |
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307 cat("Checking files filenames compatibilities with xmcs...\n") |
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308 # WHAT XCMS WILL FIND |
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309 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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310 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|") |
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311 info <- file.info(directory) |
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312 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) |
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313 files <- c(directory[!info$isdir], listed) |
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314 files_abs <- file.path(getwd(), files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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315 exists <- file.exists(files_abs) |
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316 files[exists] <- files_abs[exists] |
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317 files[exists] <- sub("//","/",files[exists]) |
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318 |
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319 # WHAT IS ON THE FILESYSTEM |
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320 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) |
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321 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] |
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322 |
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323 # COMPARISON |
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324 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { |
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325 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) |
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326 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) |
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327 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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328 |
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329 } |
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330 } |
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331 |
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332 |
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333 |
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334 ## |
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335 ## This function check if XML contains special caracters. It also checks integrity and completness. |
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336 ## |
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337 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM |
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338 checkXmlStructure <- function (directory) { |
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339 cat("Checking XML structure...\n") |
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340 |
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341 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;") |
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342 capture=system(cmd,intern=TRUE) |
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343 |
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344 if (length(capture)>0){ |
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345 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture) |
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346 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr()) |
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347 write(capture, stderr()) |
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348 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files") |
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349 } |
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350 |
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351 } |
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352 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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353 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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354 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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355 ## This function check if XML contain special characters |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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356 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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357 #@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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358 deleteXmlBadCharacters<- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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359 cat("Checking Non ASCII characters in the XML...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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360 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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361 processed=F |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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362 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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363 for (i in l){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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364 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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365 capture=suppressWarnings(system(cmd,intern=TRUE)) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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366 if (length(capture)>0){ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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367 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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368 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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369 c=system(cmd,intern=TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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370 capture="" |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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371 processed=T |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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372 } |
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373 } |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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374 if (processed) cat("\n\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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375 return(processed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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376 } |
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377 |
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378 |
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379 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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380 ## 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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381 ## |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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382 #@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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383 getMd5sum <- function (directory) { |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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384 cat("Compute md5 checksum...\n") |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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385 # WHAT XCMS WILL FIND |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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386 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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387 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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388 info <- file.info(directory) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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389 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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390 files <- c(directory[!info$isdir], listed) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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391 exists <- file.exists(files) |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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392 files <- files[exists] |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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393 |
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394 library(tools) |
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395 |
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396 #cat("\n\n") |
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397 |
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398 return(as.matrix(md5sum(files))) |
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399 } |
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400 |