Mercurial > repos > lecorguille > camera_annotate

annotate CAMERA_annotateDiffreport.r @ 39:db9bc2c27a0a draft

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author workflow4metabolomics
date Fri, 26 Jul 2019 16:00:18 -0400
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children 3d943f088143
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1 #!/usr/bin/env Rscript
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3 # ----- PACKAGE -----
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4 cat("\tSESSION INFO\n")
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6 #Import the different functions
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7 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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8 source_local("lib.r")
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10 pkgs=c("CAMERA","multtest","batch")
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11 loadAndDisplayPackages(pkgs)
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12 cat("\n\n");
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13
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14 # ----- ARGUMENTS -----
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15 cat("\tARGUMENTS INFO\n")
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17 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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18 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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20 cat("\n\n");
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23 # ----- PROCESSING INFILE -----
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24 cat("\tINFILE PROCESSING INFO\n")
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26 #image is an .RData file necessary to use xset variable given by previous tools
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27 load(args$image); args$image=NULL
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28
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29 cat("\n\n")
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32 # ----- ARGUMENTS PROCESSING -----
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33 cat("\tARGUMENTS PROCESSING INFO\n")
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35 # Save arguments to generate a report
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36 if (!exists("listOFargs")) listOFargs=list()
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37 listOFargs[[format(Sys.time(), "%y%m%d-%H:%M:%S_annotatediff")]] = args
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39 # We unzip automatically the chromatograms from the zip files.
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40 if (!exists("zipfile")) zipfile=NULL
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41 if (!exists("singlefile")) singlefile=NULL
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42 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, args)
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43 zipfile = rawFilePath$zipfile
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44 singlefile = rawFilePath$singlefile
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45 args = rawFilePath$args
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46 directory = retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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48 # Because so far CAMERA isn't compatible with the new XCMSnExp object
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49 if (exists("xdata")){
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50 xset <- getxcmsSetObject(xdata)
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51 }
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52
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53 cat("\n\n")
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56 # ----- PROCESSING INFO -----
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57 cat("\tMAIN PROCESSING INFO\n")
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58
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59 results_list=annotatediff(xset=xset,args=args,variableMetadataOutput="variableMetadata.tsv")
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60 xa=results_list$xa
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61 diffrep=results_list$diffrep
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62 variableMetadata=results_list$variableMetadata
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63
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64 cat("\n\n")
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65
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66 # ----- EXPORT -----
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67
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68 cat("\tXSET OBJECT INFO\n")
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69 print(xa)
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70 cat("\n\n")
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71
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72 #saving R data in .Rdata file to save the variables used in the present tool
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73 objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFargs","zipfile","singlefile")
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74 save(list=objects2save[objects2save %in% ls()], file="annotatediff.RData")
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75
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76 cat("\n\n")
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77
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78 cat("\tDONE\n")