Mercurial > repos > ethevenot > batchcorrection

annotate batch_correction_wrapper.R @ 1:26d058657f66 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 069d178cba334ece9c857f7718436c81c2bafb6a-dirty
author ethevenot
date Sun, 09 Apr 2017 15:27:17 -0400
parents 78cb1efd7606
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
2
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
3 ################################################################################################
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
4 # batch_correction_wrapper #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
5 # #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
6 # Author: Marion LANDI / Jean-Francois MARTIN / Melanie Petera #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
7 # User: Galaxy #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
8 # Original data: -- #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
9 # Starting date: 22-07-2014 #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
10 # Version 1: 22-07-2014 #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
11 # Version 2: 08-12-2014 #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
12 # Version 2.1: 09-01-2015 modification in Error message of sample matching #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
13 # Version 2.2: 16-03-2015 inclusion of miniTools' functions for special characters #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
14 # Version 2.90: 18-08-2015 new parameter valnull #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
15 # Version 2.91: 25-08-2016 error message improvment #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
16 # #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
17 # #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
18 # Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt (for DBC) #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
19 # Output files: graph_output.pdf ; corrected table ; diagnostic table #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
20 # #
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
21 ################################################################################################
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
22
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
23
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
24 library(batch) #necessary for parseCommandArgs function
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
25 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
26
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
27 source_local <- function(...){
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
28 argv <- commandArgs(trailingOnly = FALSE)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
29 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
30 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
31 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
32 #Import the different functions
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
33 source_local("Normalisation_QCpool.r","easyrlibrary-lib/RcheckLibrary.R","easyrlibrary-lib/miniTools.R")
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
34
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
35
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
36 ## Reading of input files
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
37 idsample=read.table(args$sampleMetadata,header=T,sep='\t',check.names=FALSE)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
38 iddata=read.table(args$dataMatrix,header=T,sep='\t',check.names=FALSE)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
39
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
40 ### Table match check
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
41 table.check <- match2(iddata,idsample,"sample")
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
42 if(length(table.check)>1){check.err(table.check)}
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
43
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
44 ### StockID
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
45 samp.id <- stockID(iddata,idsample,"sample")
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
46 iddata<-samp.id$dataMatrix ; idsample<-samp.id$Metadata ; samp.id<-samp.id$id.match
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
47
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
48 ### Checking mandatory variables
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
49 mand.check <- ""
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
50 for(mandcol in c("sampleType","injectionOrder","batch")){
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
51 if(!(mandcol%in%colnames(idsample))){
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
52 mand.check <- c(mand.check,"\nError: no '",mandcol,"' column in sample metadata.\n",
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
53 "Note: table must include this exact column name (it is case-sensitive).\n")
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
54 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
55 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
56 if(length(mand.check)>1){
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
57 mand.check <- c(mand.check,"\nFor more information, see the help section or:",
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
58 "\n http://workflow4metabolomics.org/sites/",
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
59 "workflow4metabolomics.org/files/files/w4e-2016-data_processing.pdf\n")
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
60 check.err(mand.check)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
61 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
62
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
63 ### Formating
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
64 idsample[[1]]=make.names(idsample[[1]])
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
65 dimnames(iddata)[[1]]=iddata[[1]]
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
66
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
67 ### Transposition of ions data
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
68 idTdata=t(iddata[,2:dim(iddata)[2]])
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
69 idTdata=data.frame(dimnames(idTdata)[[1]],idTdata)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
70
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
71 ### Merge of 2 files (ok even if the two dataframe are not sorted on the same key)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
72 id=merge(idsample, idTdata, by.x=1, by.y=1)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
73
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
74 id$batch=as.factor(id$batch)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
75 ids=id[id$sampleType == 'pool' | id$sampleType == 'sample',]
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
76 nbid=dim(idsample)[2]
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
77
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
78 ### Checking the number of sample and pool
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
79
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
80 # least 2 samples
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
81 if(length(which(ids$sampleType == "sample"))<2){
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
82 table.check <- c(table.check,"\nError: less than 2 samples specified in sample metadata.",
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
83 "\nMake sure this is not due to errors in sampleType coding.\n")
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
84 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
85
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
86 # least 2 pools per batch for all batchs
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
87 B <- rep(0,length(levels(ids$batch)))
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
88 for(nbB in length(levels(ids$batch))){
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
89 B[nbB]<-length(which(ids[which(ids$batch==(levels(ids$batch)[nbB])),]$sampleType == "pool"))
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
90 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
91 if(length(which(B>1))==0){
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
92 table.check <- c(table.check,"\nError: less than 2 pools specified in each batch in sample metadata.",
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
93 "\nMake sure this is not due to errors in sampleType coding.\n")
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
94 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
95
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
96 ### Factor of interest
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
97 factbio=args$ref_factor
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
98
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
99
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
100 if(args$analyse == "batch_correction") {
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
101 ## Reading of Metadata Ions file
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
102 metaion=read.table(args$variableMetadata,header=T,sep='\t',check.names=FALSE)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
103 ## Table match check
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
104 table.check <- c(table.check,match2(iddata,metaion,"variable"))
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
105 check.err(table.check)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
106
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
107 ## variables
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
108 detail=args$detail
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
109 method=args$method
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
110
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
111 ## outputs
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
112 outlog=args$graph_output
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
113
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
114 ## Launch
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
115 res = norm_QCpool(ids,nbid,outlog,factbio,metaion,detail,F,F,method,args$span,args$valnull)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
116 save(res, file=args$rdata_output)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
117 write.table(reproduceID(res[[1]],res[[3]],"sample",samp.id)$dataMatrix, file=args$dataMatrix_out, sep = '\t', row.names=F, quote=F)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
118 write.table(res[[2]], file=args$variableMetadata_out, sep = '\t', row.names=F, quote=F)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
119 }else{
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
120 ## error check
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
121 check.err(table.check)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
122
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
123 ## outputs
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
124 out_graph_pdf=args$out_graph_pdf
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
125 out_preNormSummary=args$out_preNormSummary
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
126
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
127 ## Launch
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
128 plotsituation(ids,nbid,out_graph_pdf,out_preNormSummary,factbio,args$span)
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
129 }
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
130
78cb1efd7606 planemo upload for repository https://github.com/workflow4metabolomics/batch_correction.git commit 400138235741cbb21fd7c7ddeeb572235fa769c2-dirty
ethevenot
parents:
diff changeset
131 rm(args)