Mercurial > repos > sblanck > smagexp
annotate MetaRNASeq.R @ 22:c44bb4ec5c78 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit ecb5d3451f1623e0cc649ac5197e66995ce19eef-dirty
| author | sblanck |
|---|---|
| date | Thu, 22 Feb 2018 10:21:12 -0500 |
| parents | ef7d98f9eb51 |
| children | cb29ad7d75a5 |
| rev | line source |
|---|---|
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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1 #!/usr/bin/env Rscript |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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2 # setup R error handling to go to stderr |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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3 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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4 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings. |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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6 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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7 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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8 library("optparse") |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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9 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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10 ##### Read options |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
parents:
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11 option_list=list( |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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12 make_option("--input",type="character",default="NULL",help="list of rdata objects containing eset objects"), |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
parents:
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13 make_option("--result",type="character",default=NULL,help="text file containing result of the meta-analysis"), |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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14 make_option("--htmloutput",type="character",default=NULL,help="Output html report"), |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
parents:
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15 make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
parents:
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16 make_option("--htmltemplate",type="character",default=NULL,help="html template)") |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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17 ); |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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18 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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19 opt_parser = OptionParser(option_list=option_list); |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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20 opt = parse_args(opt_parser); |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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21 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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22 if(is.null(opt$input)){ |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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23 print_help(opt_parser) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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24 stop("input required.", call.=FALSE) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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25 } |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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26 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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27 #loading libraries |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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28 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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29 suppressPackageStartupMessages(require(affy)) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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30 suppressPackageStartupMessages(require(annaffy)) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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31 suppressPackageStartupMessages(require(VennDiagram)) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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32 suppressPackageStartupMessages(require(GEOquery)) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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33 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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34 listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) ) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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35 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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36 listfiles=vector() |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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37 listfilenames=vector() |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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38 |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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39 for (i in 1:length(listInput)) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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40 { |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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41 inputFileInfo <- unlist( strsplit( listInput[i], ';' ) ) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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42 listfiles=c(listfiles,inputFileInfo[1]) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
parents:
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43 listfilenames=c(listfilenames,inputFileInfo[2]) |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
sblanck
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44 } |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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45 |
| 2 | 46 cargs <- commandArgs() |
| 47 cargs <- cargs[(which(cargs == "--args")+1):length(cargs)] | |
| 48 nbargs=length(cargs) | |
| 49 listfiles=vector() | |
| 50 listfilenames=vector() | |
| 51 for (i in seq(1,nbargs-6,2)) { | |
| 52 listfiles=c(listfiles,cargs[[i]]) | |
| 53 listfilenames=c(listfilenames,cargs[[i+1]]) | |
| 54 } | |
| 55 #mod<-cargs[[length(cargs) - 6]] | |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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56 outputfile <- opt$result |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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57 result.html = opt$htmloutput |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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58 html.files.path=opt$htmloutputpath |
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e5a94bc69bd6
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit da1436252b5db4e90c39c95140558f0f93544160
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parents:
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59 result.template=opt$htmltemplate |
| 2 | 60 |
| 61 alpha=0.05 | |
| 62 | |
| 63 #print(comparison) | |
| 64 | |
| 65 listData=lapply(listfiles,read.table) | |
| 66 orderData=lapply(listData, function(x) x[order(x[1]), ]) | |
| 67 rawpval=lapply(orderData,function(x) x[6]) | |
| 68 rawpval=lapply(rawpval, function(x) as.numeric(unlist(x))) | |
| 69 | |
| 70 DE=list() | |
| 71 DE=lapply(orderData, function(x) ifelse(x[7]<=0.05,1,0)) | |
| 72 | |
| 73 FC=list() | |
| 74 FC=lapply(orderData, function(x) x[3]) | |
| 75 | |
| 76 DE=as.data.frame(DE) | |
| 77 colnames(DE)=listfilenames | |
| 78 FC=as.data.frame(FC) | |
| 79 colnames(FC)=listfilenames | |
| 80 # the comparison must only have two values and the conds must | |
| 81 # be a vector from those values, at least one of each. | |
| 82 | |
| 83 #if (length(comparison) != 2) { | |
| 84 # stop("Comparison type must be a tuple: ", cargs[length(cargs) - 8]) | |
| 85 #} | |
| 86 | |
| 87 sink("/dev/null") | |
| 88 dir.create(html.files.path, recursive=TRUE) | |
| 89 #library(DESeq) | |
| 90 #library(HTSFilter) | |
| 91 | |
| 92 #DE=list() | |
| 93 #FC=list() | |
| 94 #i=1 | |
| 95 | |
| 96 # Open the html output file | |
| 97 #file.conn = file(diag.html, open="w") | |
| 98 | |
| 99 #writeLines( c("<html><body>"), file.conn) | |
| 100 | |
| 101 # Perform deseq analysis on each study | |
| 102 #for(i in 1:length(listfiles)) | |
| 103 #{ | |
| 104 # f=listfiles[i] | |
| 105 # fname=listfilenames[i] | |
| 106 # study_name=unlist(strsplit(fname,"[.]"))[1] | |
| 107 # print(paste0("study.name ",study_name)) | |
| 108 # d <- read.table(f, sep=" ", header=TRUE, row.names=1) | |
| 109 # conds<-sapply(strsplit(colnames(d),"[.]"),FUN=function(x) x[1]) | |
| 110 # if (length(unique(conds)) != 2) { | |
| 111 # warning(as.data.frame(strsplit(colnames(d),"[.]"))) | |
| 112 # stop("You can only have two columns types: ", paste(conds,collapse=" ")) | |
| 113 # } | |
| 114 # if (!identical(sort(comparison), sort(unique(conds)))) { | |
| 115 # stop("Column types must use the two names from Comparison type, and vice versa. Must have at least one of each in the Column types.\nColumn types: ", cargs[2], "\n", "Comparison type: ", cargs[3]) | |
| 116 # } | |
| 117 # if (length(d) != length(conds)) { | |
| 118 # stop("Number of total sample columns in counts file must correspond to the columns types field. E.g. if column types is 'kidney,kidney,liver,liver' then number of sample columns in counts file must be 4 as well.") | |
| 119 # } | |
| 120 # | |
| 121 # cds <- newCountDataSet(d, conds) | |
| 122 # cds <- estimateSizeFactors(cds) | |
| 123 # | |
| 124 # cdsBlind <- estimateDispersions( cds, method="blind" ) | |
| 125 # | |
| 126 # if (length(conds) != 2) { | |
| 127 # cds <- estimateDispersions( cds ) | |
| 128 # norep = FALSE | |
| 129 # } | |
| 130 # | |
| 131 # if (length(conds) == 2) { | |
| 132 # cds <- estimateDispersions( cds, method=method, sharingMode=mod, fitType="parametric" ) | |
| 133 # norep = TRUE | |
| 134 # } | |
| 135 # | |
| 136 # filter<-HTSFilter(cds, plot=FALSE) | |
| 137 # cds.filter<-filter$filteredData | |
| 138 # on.index<-which(filter$on==1) | |
| 139 # | |
| 140 # res<-as.data.frame(matrix(NA,nrow=nrow(cds),ncol=ncol(cds))) | |
| 141 # nbT <- nbinomTest(cds.filter, comparison[1], comparison[2]) | |
| 142 # colnames(res)<-colnames(nbT) | |
| 143 # res[on.index,]<-nbT | |
| 144 # #write.table(res[order(res$padj), ], file=outputfile, quote=FALSE, row.names=FALSE, sep="\t") | |
| 145 # | |
| 146 # | |
| 147 # temp.pval.plot = file.path( html.files.path, paste("PvalHist",i,".png",sep="")) | |
| 148 # png( temp.pval.plot, width=500, height=500 ) | |
| 149 # hist(res$pval, breaks=100, col="skyblue", border="slateblue", main="") | |
| 150 # dev.off() | |
| 151 # | |
| 152 # writeLines( c("<h2>P-value histogram for ",study_name,"</h2>"), file.conn) | |
| 153 # writeLines( c("<img src='PvalHist",i,".png'><br/><br/>"), file.conn) | |
| 154 # | |
| 155 # #on enregistre la p-value | |
| 156 # rawpval[[study_name]]<-res$pval | |
| 157 # DE[[study_name]]<-ifelse(res$padj<=alpha,1,0) | |
| 158 # FC[[study_name]]<-res$log2FoldChange | |
| 159 # | |
| 160 # i=i+1 | |
| 161 #} | |
| 162 | |
| 163 | |
| 164 # combinations | |
| 165 library(metaRNASeq) | |
| 166 fishcomb<-fishercomb(rawpval, BHth=alpha) | |
| 167 warning(length(rawpval)) | |
| 168 invnormcomb<-invnorm(rawpval, nrep=c(8,8), BHth=alpha) | |
| 169 #DE[["fishercomb"]]<-ifelse(fishcomb$adjpval<=alpha,1,0) | |
| 170 #DE[["invnormcomb"]]<-ifelse(invnormcomb$adjpval<=alpha,1,0) | |
| 171 | |
| 172 signsFC<-mapply(FC,FUN=function(x) sign(x)) | |
| 173 sumsigns<-apply(signsFC,1,sum) | |
| 174 commonsgnFC<-ifelse(abs(sumsigns)==dim(signsFC)[2],sign(sumsigns),0) | |
| 175 | |
| 176 DEresults <- data.frame(DE=DE,"DE.fishercomb"=ifelse(fishcomb$adjpval<=alpha,1,0),"DE.invnorm"=ifelse(invnormcomb$adjpval<=alpha,1,0)) | |
| 177 | |
| 178 unionDE <- unique(c(fishcomb$DEindices,invnormcomb$DEindices)) | |
| 179 FC.selecDE <- data.frame(DEresults[unionDE,],FC[unionDE,],signFC=commonsgnFC[unionDE]) | |
| 180 keepDE <- FC.selecDE[which(abs(FC.selecDE$signFC)==1),] | |
| 181 | |
| 182 fishcomb_de <- rownames(keepDE)[which(keepDE[,"DE.fishercomb"]==1)] | |
| 183 invnorm_de <- rownames(keepDE)[which(keepDE[,"DE.invnorm"]==1)] | |
| 184 indstudy_de = list() | |
| 185 for (i in 1:length(listfiles)) { | |
| 186 currentIndstudy_de = rownames(keepDE)[which(keepDE[,i]==1)] | |
| 187 indstudy_de[[listfilenames[i]]]=currentIndstudy_de | |
| 188 } | |
| 189 | |
| 190 IDDIRRfishcomb=IDD.IRR(fishcomb_de,indstudy_de) | |
| 191 IDDIRRinvnorm=IDD.IRR(invnorm_de,indstudy_de) | |
| 192 | |
| 193 #conflits<-data.frame(ID=listData[[1]][rownames(DEresults),1],Fishercomb=DEresults[["DE.fishercomb"]],Invnormcomb=DEresults[["DE.invnorm"]],sign=commonsgnFC) | |
| 194 conflits<-data.frame(ID=listData[[1]][rownames(DEresults),1],DE=DEresults,FC=FC,signFC=commonsgnFC) | |
| 195 #write DE outputfile | |
| 196 write.table(conflits, outputfile,sep="\t",,row.names=FALSE) | |
| 197 library(VennDiagram) | |
| 198 DE_num=apply(DEresults, 2, FUN=function(x) which(x==1)) | |
| 199 venn.plot<-venn.diagram(x=as.list(DE_num),filename=NULL, col="black", fill=1:length(DE_num)+1,alpha=0.6) | |
| 200 temp.venn.plot = file.path( html.files.path, paste("venn.png")) | |
| 201 png(temp.venn.plot,width=500,height=500) | |
| 202 grid.draw(venn.plot) | |
| 203 dev.off() | |
| 204 | |
| 205 library(jsonlite) | |
| 206 matrixConflits=as.matrix(conflits) | |
| 207 datajson=toJSON(matrixConflits,pretty = TRUE) | |
| 208 summaryFishcombjson=toJSON(as.matrix(t(IDDIRRfishcomb)),pretty = TRUE) | |
| 209 summaryinvnormjson=toJSON(as.matrix(t(IDDIRRinvnorm)),pretty = TRUE) | |
| 210 | |
| 211 | |
| 212 #vennsplit=strsplit(result.venn,split="/")[[1]] | |
| 213 #venn=paste0("./",vennsplit[length(vennsplit)]) | |
| 214 | |
| 215 | |
| 216 vennFilename="venn.png" | |
| 217 vennFile=file.path(html.files.path,vennFilename) | |
| 218 htmlfile=readChar(result.template, file.info(result.template)$size) | |
| 219 htmlfile=gsub(x=htmlfile,pattern = "###DATAJSON###",replacement = datajson, fixed = TRUE) | |
| 220 htmlfile=gsub(x=htmlfile,pattern = "###FISHSUMMARYJSON###",replacement = summaryFishcombjson, fixed = TRUE) | |
| 221 htmlfile=gsub(x=htmlfile,pattern = "###INVSUMMARYJSON###",replacement = summaryinvnormjson, fixed = TRUE) | |
| 222 htmlfile=gsub(x=htmlfile,pattern = "###VENN###",replacement = vennFilename, fixed = TRUE) | |
| 223 write(htmlfile,result.html) | |
| 224 | |
| 225 #library(VennDiagram) | |
| 226 #flog.threshold(ERROR) | |
| 227 # | |
| 228 ##venn.plot<-venn.diagram(x = c(res[c(1:(length(res)-3))],meta=list(res$Meta)),filename = v, col = "black", fill = c(1:(length(res)-2)), margin=0.05, alpha = 0.6,imagetype = "png") | |
| 229 #dir.create(result.path, showWarnings = TRUE, recursive = FALSE) | |
| 230 # | |
| 231 #showVenn<-function(liste,file) | |
| 232 #{ | |
| 233 # venn.plot<-venn.diagram(x = liste, | |
| 234 # filename = vennFilename, col = "black", | |
| 235 # fill = 1:length(liste)+1, | |
| 236 # margin=0.05, alpha = 0.6,imagetype = "png") | |
| 237 ## png(file); | |
| 238 ## grid.draw(venn.plot); | |
| 239 ## dev.off(); | |
| 240 # | |
| 241 #} | |
| 242 # | |
| 243 #l=list() | |
| 244 #for(i in 1:length(esets)) | |
| 245 #{ | |
| 246 # l[[paste("study",i,sep="")]]<-res[[i]] | |
| 247 #} | |
| 248 #l[["Meta"]]=res[[length(res)-1]] | |
| 249 #showVenn(l,vennFile) | |
| 250 #file.copy(vennFilename,result.path) | |
| 251 | |
| 252 | |
| 253 #writeLines( c("<h2>Venn Plot</h2>"), file.conn) | |
| 254 #writeLines( c("<img src='venn.png'><br/><br/>"), file.conn) | |
| 255 #writeLines( c("</body></html>"), file.conn) | |
| 256 #close(file.conn) | |
| 257 #print("passe6") | |
| 258 #sink(NULL) |