Mercurial > repos > theo.collard > ballgown_wrapper
comparison ballgown.R @ 6:c637c3bf6781 draft
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author | theo.collard |
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date | Wed, 26 Apr 2017 08:45:30 -0400 |
parents | 940701e8bc59 |
children | 4290f0f3d908 |
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5:5e80570024ed | 6:c637c3bf6781 |
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1 #!/usr/bin/Rscript | |
2 | |
3 # Enabling commands line arguments. Using optparse which allows to use options. | |
4 # ---------------------------------------------------------------------------------------- | |
5 | |
6 suppressMessages(library(optparse, warn.conflicts = FALSE)) | |
7 opt_list=list( | |
8 make_option(c("-d", "--directory"), type="character", default=NULL, help="directory containing the samples", metavar="character"), | |
9 make_option(c("-p", "--phendat"), type="character", default=NULL, help="phenotype data(must be a .csv file)", metavar="character"), | |
10 make_option(c("-t","--outputtranscript"), type="character", default="output_transcript.csv", help="output_transcript.csv: contains the transcripts of the expirements", metavar="character"), | |
11 make_option(c("-g","--outputgenes"), type="character", default="output_genes.csv", help="output_genes.csv: contains the genes of the expirements", metavar="character"), | |
12 make_option(c("-e","--texpression"), type="double", default="0.5", help="transcripts expression filter", metavar="character"), | |
13 make_option(c("--bgout"), type="character", default="", help="save the ballgown object created in the process", metavar="character") | |
14 ) | |
15 opt_parser=OptionParser(option_list=opt_list) | |
16 opt=parse_args(opt_parser) | |
17 | |
18 # Loading required libraries. suppressMessages() remove all noisy attachement messages | |
19 # ---------------------------------------------------------------------------------------- | |
20 | |
21 suppressMessages(library(ballgown, warn.conflicts = FALSE)) | |
22 suppressMessages(library(genefilter, warn.conflicts = FALSE)) | |
23 suppressMessages(library(dplyr, warn.conflicts = FALSE)) | |
24 | |
25 # Setup for the tool with some bases variables. | |
26 # ---------------------------------------------------------------------------------------- | |
27 | |
28 | |
29 filtstr = opt$texpression | |
30 pdat = 2 | |
31 phendata = read.csv(opt$phendat) | |
32 setwd(opt$dir) | |
33 | |
34 # Checking if the pdata file has the right samples names. | |
35 # ---------------------------------------------------------------------------------------- | |
36 | |
37 if (all(phendata$ids == list.files(".")) != TRUE) | |
38 { | |
39 stop("Your phenotype data table does not match the samples names. ") | |
40 } | |
41 | |
42 # Creation of the ballgown object based on data | |
43 # ---------------------------------------------------------------------------------------- | |
44 bgi = ballgown(dataDir= "." , samplePattern="", pData = phendata, verbose = FALSE) | |
45 | |
46 # Filter the genes with an expression superior to the input filter | |
47 # ---------------------------------------------------------------------------------------- | |
48 bgi_filt= subset(bgi, paste("rowVars(texpr(bgi)) >",filtstr), genomesubset = TRUE) | |
49 | |
50 # Creating the variables containing the transcripts and the genes and sorting them through the arrange() command. | |
51 # Checking if there's one or more adjust variables in the phenotype data file | |
52 # ---------------------------------------------------------------------------------------- | |
53 | |
54 if (ncol(pData(bgi))<=3) { | |
55 results_transcripts=stattest(bgi_filt,feature = "transcript", covariate = colnames(pData(bgi))[pdat], adjustvars = colnames(pData(bgi)[pdat+1]), getFC = TRUE, meas = "FPKM") | |
56 results_genes=stattest(bgi_filt,feature = "gene", covariate = colnames(pData(bgi))[pdat], adjustvars = colnames(pData(bgi)[pdat+1]), getFC = TRUE, meas = "FPKM") | |
57 } else { | |
58 results_transcripts=stattest(bgi_filt,feature = "transcript", covariate = colnames(pData(bgi))[pdat], adjustvars = c(colnames(pData(bgi)[pdat+1:ncol(pData(bgi))])), getFC = TRUE, meas = "FPKM") | |
59 results_genes=stattest(bgi_filt,feature = "gene", covariate = colnames(pData(bgi))[pdat], adjustvars = c(colnames(pData(bgi)[pdat+1:ncol(pData(bgi))])), getFC = TRUE, meas = "FPKM") | |
60 } | |
61 | |
62 results_transcripts = data.frame(geneNames=ballgown::geneNames(bgi_filt), geneIDs=ballgown::geneIDs(bgi_filt), results_transcripts) | |
63 results_transcripts = arrange(results_transcripts,pval) | |
64 results_genes = arrange(results_genes,pval) | |
65 | |
66 # Main output of the wrapper, two .csv files containing the genes and transcripts with their qvalue and pvalue | |
67 #This part also output the data of the ballgown object created in the process and save it in a R data file | |
68 # ---------------------------------------------------------------------------------------- | |
69 write.csv(results_transcripts, opt$outputtranscript, row.names = FALSE) | |
70 write.csv(results_genes, opt$outputgenes, row.names = FALSE) | |
71 if (opt$bgout != ""){ | |
72 save(bgi, file=opt$bgout) | |
73 } |