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annotate deseq2.R @ 3:1ae1da9a5e66 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 521ea70d49fee701db4d832823644c8c3050f8f2-dirty
author iuc
date Fri, 04 Sep 2015 07:15:37 -0400
parents 5b1ce9db498e
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5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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1 # A command-line interface to DESeq2 for use with Galaxy
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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2 # written by Bjoern Gruening and modified by Michael Love 2015.01.11
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3 #
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4 # one of these arguments is required:
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5 #
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6 # 'factors' a JSON list object from Galaxy
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7 #
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8 # 'sample_table' is a sample table as described in ?DESeqDataSetFromHTSeq
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9 # with columns: sample name, filename, then factors (variables)
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10 #
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11 # the output file has columns:
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12 #
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13 # baseMean (mean normalized count)
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14 # log2FoldChange (by default a moderated LFC estimate)
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15 # lfcSE (the standard error)
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16 # stat (the Wald statistic)
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17 # pvalue (p-value from comparison of Wald statistic to a standard Normal)
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18 # padj (adjusted p-value, Benjamini Hochberg correction on genes which pass the mean count filter)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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19 #
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20 # the first variable in 'factors' and first column in 'sample_table' will be the primary factor.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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21 # the levels of the primary factor are used in the order of appearance in factors or in sample_table.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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22 #
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23 # by default, levels in the order A,B,C produces a single comparison of B vs A, to a single file 'outfile'
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24 #
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25 # for the 'many_contrasts' flag, levels in the order A,B,C produces comparisons C vs A, B vs A, C vs B,
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26 # to a number of files using the 'outfile' prefix: 'outfile.condition_C_vs_A' etc.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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27 # all plots will still be sent to a single PDF, named by the arg 'plots', with extra pages.
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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28 #
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29 # fit_type is an integer valued argument, with the options from ?estimateDisperions
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30 # 1 "parametric"
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31 # 2 "local"
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32 # 3 "mean"
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33
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34 # setup R error handling to go to stderr
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35 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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36
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37 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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38 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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39
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40 library("getopt")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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41 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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42 args <- commandArgs(trailingOnly = TRUE)
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43
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44 # get options, using the spec as defined by the enclosed list.
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45 # we read the options from the default: commandArgs(TRUE).
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46 spec <- matrix(c(
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47 "quiet", "q", 0, "logical",
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48 "help", "h", 0, "logical",
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49 "outfile", "o", 1, "character",
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50 "factors", "f", 1, "character",
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51 "plots" , "p", 1, "character",
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52 "sample_table", "s", 1, "character",
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53 "fit_type", "t", 1, "integer",
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54 "many_contrasts", "m", 0, "logical",
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55 "outlier_replace_off" , "a", 0, "logical",
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56 "outlier_filter_off" , "b", 0, "logical",
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57 "auto_mean_filter_off", "c", 0, "logical",
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58 "beta_prior_off", "d", 0, "logical"),
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59 byrow=TRUE, ncol=4)
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60 opt <- getopt(spec)
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61
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62 # if help was asked for print a friendly message
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63 # and exit with a non-zero error code
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64 if (!is.null(opt$help)) {
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65 cat(getopt(spec, usage=TRUE))
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66 q(status=1)
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67 }
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68
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69 # enforce the following required arguments
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70 if (is.null(opt$outfile)) {
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71 cat("'outfile' is required\n")
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72 q(status=1)
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73 }
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74 if (is.null(opt$sample_table) & is.null(opt$factors)) {
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75 cat("'factors' or 'sample_table' is required\n")
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76 q(status=1)
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77 }
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78
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79 verbose <- if (is.null(opt$quiet)) {
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80 TRUE
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81 } else {
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82 FALSE
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83 }
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84
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85 suppressPackageStartupMessages({
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86 library("DESeq2")
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87 library("RColorBrewer")
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88 library("gplots")
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89 })
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90
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91 # build or read sample table
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92
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93 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
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94
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95 # switch on if 'factors' was provided:
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96 if (!is.null(opt$factors)) {
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97 library("rjson")
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98 parser <- newJSONParser()
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99 parser$addData(opt$factors)
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100 factorList <- parser$getObject()
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101 factors <- sapply(factorList, function(x) x[[1]])
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102 primaryFactor <- factors[1]
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103 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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104 sampleTable <- data.frame(sample=basename(filenamesIn), filename=filenamesIn, row.names=filenamesIn)
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105 for (factor in factorList) {
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106 factorName <- trim(factor[[1]])
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107 sampleTable[[factorName]] <- character(nrow(sampleTable))
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108 lvls <- sapply(factor[[2]], function(x) names(x))
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109 for (i in seq_along(factor[[2]])) {
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110 files <- factor[[2]][[i]][[1]]
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111 sampleTable[files,factorName] <- trim(lvls[i])
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112 }
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113 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls)
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114 }
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115 rownames(sampleTable) <- sampleTable$sample
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116 } else {
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117 # read the sample_table argument
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118 # this table is described in ?DESeqDataSet
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119 # one column for the sample name, one for the filename, and
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120 # the remaining columns for factors in the analysis
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121 sampleTable <- read.delim(opt$sample_table)
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122 factors <- colnames(sampleTable)[-c(1:2)]
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123 for (factor in factors) {
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124 lvls <- unique(as.character(sampleTable[[factor]]))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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125 sampleTable[[factor]] <- factor(sampleTable[[factor]], levels=lvls)
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126 }
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127 }
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128
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129 primaryFactor <- factors[1]
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130 designFormula <- as.formula(paste("~", paste(rev(factors), collapse=" + ")))
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131
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132 if (verbose) {
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133 cat("DESeq2 run information\n\n")
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134 cat("sample table:\n")
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135 print(sampleTable[,-c(1:2),drop=FALSE])
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136 cat("\ndesign formula:\n")
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137 print(designFormula)
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138 cat("\n\n")
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139 }
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140
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141 # these are plots which are made once for each analysis
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142 generateGenericPlots <- function(dds, factors) {
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143 rld <- rlog(dds)
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144 print(plotPCA(rld, intgroup=rev(factors)))
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145 # need meaningful labels, because from Galaxy, sample names are random
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146 labs <- paste0(seq_len(ncol(dds)), ": ", do.call(paste, as.list(colData(dds)[factors])))
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147 dat <- assay(rld)
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148 colnames(dat) <- labs
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149 distsRL <- dist(t(dat))
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150 mat <- as.matrix(distsRL)
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151 hc <- hclust(distsRL)
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152 hmcol <- colorRampPalette(brewer.pal(9, "GnBu"))(100)
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153 heatmap.2(mat, Rowv=as.dendrogram(hc), symm=TRUE, trace="none", col = rev(hmcol),
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154 main="Sample-to-sample distances", margin=c(13,13))
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155 plotDispEsts(dds, main="Dispersion estimates")
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156 }
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157
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158 # these are plots which can be made for each comparison, e.g.
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159 # once for C vs A and once for B vs A
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160 generateSpecificPlots <- function(res, threshold, title_suffix) {
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161 use <- res$baseMean > threshold
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162 if (sum(!use) == 0) {
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163 h <- hist(res$pvalue, breaks=0:50/50, plot=FALSE)
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164 barplot(height = h$counts,
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165 col = "powderblue", space = 0, xlab="p-values", ylab="frequency",
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166 main=paste("Histogram of p-values for",title_suffix))
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167 text(x = c(0, length(h1$counts)), y = 0, label=paste(c(0,1)), adj=c(0.5,1.7), xpd=NA)
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168 } else {
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169 h1 <- hist(res$pvalue[!use], breaks=0:50/50, plot=FALSE)
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170 h2 <- hist(res$pvalue[use], breaks=0:50/50, plot=FALSE)
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171 colori <- c("filtered (low count)"="khaki", "not filtered"="powderblue")
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172 barplot(height = rbind(h1$counts, h2$counts), beside = FALSE,
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173 col = colori, space = 0, xlab="p-values", ylab="frequency",
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174 main=paste("Histogram of p-values for",title_suffix))
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175 text(x = c(0, length(h1$counts)), y = 0, label=paste(c(0,1)), adj=c(0.5,1.7), xpd=NA)
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176 legend("topright", fill=rev(colori), legend=rev(names(colori)), bg="white")
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177 }
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178 plotMA(res, main= paste("MA-plot for",title_suffix), ylim=range(res$log2FoldChange, na.rm=TRUE))
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179 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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180
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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181 if (verbose) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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182 cat(paste("primary factor:",primaryFactor,"\n"))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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183 if (length(factors) > 1) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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184 cat(paste("other factors in design:",paste(factors[-length(factors)],collapse=","),"\n"))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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185 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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186 cat("\n---------------------\n")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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187 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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188
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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189 # if JSON input from Galaxy, path is absolute
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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190 # otherwise, from sample_table, assume it is relative
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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191 dir <- if (is.null(opt$factors)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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192 "."
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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193 } else {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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194 ""
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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195 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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196
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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197 # construct the object
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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198 dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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199 directory = dir,
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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200 design = designFormula)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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201
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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202 if (verbose) cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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203
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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204 # optional outlier behavior
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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205 if (is.null(opt$outlier_replace_off)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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206 minRep <- 7
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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207 } else {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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208 minRep <- Inf
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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209 if (verbose) cat("outlier replacement off\n")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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210 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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211 if (is.null(opt$outlier_filter_off)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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212 cooksCutoff <- TRUE
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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213 } else {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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214 cooksCutoff <- FALSE
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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215 if (verbose) cat("outlier filtering off\n")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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216 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
217
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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218 # optional automatic mean filtering
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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219 if (is.null(opt$auto_mean_filter_off)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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220 independentFiltering <- TRUE
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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221 } else {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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222 independentFiltering <- FALSE
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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223 if (verbose) cat("automatic filtering on the mean off\n")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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224 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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225
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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226 # shrinkage of LFCs
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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227 if (is.null(opt$beta_prior_off)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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228 betaPrior <- TRUE
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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229 } else {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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230 betaPrior <- FALSE
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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231 if (verbose) cat("beta prior off\n")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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232 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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233
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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234 # dispersion fit type
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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235 if (is.null(opt$fit_type)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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236 fitType <- "parametric"
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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237 } else {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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238 fitType <- c("parametric","local","mean")[opt$fit_type]
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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239 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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240
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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241 if (verbose) cat(paste("using disperion fit type:",fitType,"\n"))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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242
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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243 # run the analysis
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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244 dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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245
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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246 # create the generic plots and leave the device open
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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247 if (!is.null(opt$plots)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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248 if (verbose) cat("creating plots\n")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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249 pdf(opt$plots)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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250 generateGenericPlots(dds, factors)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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251 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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252
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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253 n <- nlevels(colData(dds)[[primaryFactor]])
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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254 allLevels <- levels(colData(dds)[[primaryFactor]])
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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255
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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256 if (is.null(opt$many_contrasts)) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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257 # only contrast the first and second level of the primary factor
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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258 ref <- allLevels[1]
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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259 lvl <- allLevels[2]
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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260 res <- results(dds, contrast=c(primaryFactor, lvl, ref),
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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261 cooksCutoff=cooksCutoff,
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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262 independentFiltering=independentFiltering)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
263 if (verbose) {
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
parents:
diff changeset
264 cat("summary of results\n")
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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diff changeset
265 cat(paste0(primaryFactor,": ",lvl," vs ",ref,"\n"))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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266 print(summary(res))
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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267 }
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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268 resSorted <- res[order(res$padj),]
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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269 outDF <- as.data.frame(resSorted)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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270 outDF$geneID <- rownames(outDF)
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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271 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
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272 filename <- opt$outfile
5b1ce9db498e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 76d0758966bde7c15f5224913cee5e8ce28314ff
iuc
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273 write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
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274 if (independentFiltering) {
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275 threshold <- unname(attr(res, "filterThreshold"))
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276 } else {
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277 threshold <- 0
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278 }
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279 title_suffix <- paste0(primaryFactor,": ",lvl," vs ",ref)
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280 if (!is.null(opt$plots)) {
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281 generateSpecificPlots(res, threshold, title_suffix)
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282 }
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283 } else {
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284 # rotate through the possible contrasts of the primary factor
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285 # write out a sorted table of results with the contrast as a suffix
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286 # add contrast specific plots to the device
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287 for (i in seq_len(n-1)) {
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288 ref <- allLevels[i]
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289 contrastLevels <- allLevels[(i+1):n]
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290 for (lvl in contrastLevels) {
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291 res <- results(dds, contrast=c(primaryFactor, lvl, ref),
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292 cooksCutoff=cooksCutoff,
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293 independentFiltering=independentFiltering)
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294 resSorted <- res[order(res$padj),]
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295 outDF <- as.data.frame(resSorted)
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296 outDF$geneID <- rownames(outDF)
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297 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
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298 filename <- paste0(opt$outfile,".",primaryFactor,"_",lvl,"_vs_",ref)
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299 write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
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300 if (independentFiltering) {
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301 threshold <- unname(attr(res, "filterThreshold"))
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302 } else {
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303 threshold <- 0
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304 }
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305 title_suffix <- paste0(primaryFactor,": ",lvl," vs ",ref)
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306 if (!is.null(opt$plots)) {
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307 generateSpecificPlots(res, threshold, title_suffix)
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308 }
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309 }
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310 }
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311 }
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312
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313 # close the plot device
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314 if (!is.null(opt$plots)) {
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315 cat("closing plot device\n")
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316 dev.off()
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317 }
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318
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319 cat("Session information:\n\n")
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320
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321 sessionInfo()
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322