Mercurial > repos > iuc > deseq2

annotate deseq2.R @ 16:a416957ee305 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 81fa5b04b9ba9d4b1b59192af0adb1e1e18ca22b
author iuc
date Fri, 03 Aug 2018 17:23:46 -0400
parents 9a616afdbda5
children d9e5cadc7f0b
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1 #!/usr/bin/env Rscript
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2
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3 # A command-line interface to DESeq2 for use with Galaxy
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4 # written by Bjoern Gruening and modified by Michael Love 2016.03.30
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5 #
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6 # This argument is required:
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7 #
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8 # 'factors' a JSON list object from Galaxy
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9 #
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10 # the output file has columns:
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11 #
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12 # baseMean (mean normalized count)
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13 # log2FoldChange (by default a moderated LFC estimate)
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14 # lfcSE (the standard error)
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15 # stat (the Wald statistic)
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16 # pvalue (p-value from comparison of Wald statistic to a standard Normal)
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17 # padj (adjusted p-value, Benjamini Hochberg correction on genes which pass the mean count filter)
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18 #
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19 # the first variable in 'factors' will be the primary factor.
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20 # the levels of the primary factor are used in the order of appearance in factors.
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21 #
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22 # 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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23 #
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24 # 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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25 # to a number of files using the 'outfile' prefix: 'outfile.condition_C_vs_A' etc.
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26 # all plots will still be sent to a single PDF, named by the arg 'plots', with extra pages.
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27 #
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28 # fit_type is an integer valued argument, with the options from ?estimateDisperions
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29 # 1 "parametric"
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30 # 2 "local"
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31 # 3 "mean"
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33 # setup R error handling to go to stderr
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34 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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36 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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37 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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39 library("getopt")
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40 library("tools")
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41 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
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42 args <- commandArgs(trailingOnly = TRUE)
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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 "countsfile", "n", 1, "character",
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51 "header", "H", 0, "logical",
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52 "factors", "f", 1, "character",
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53 "files_to_labels", "l", 1, "character",
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54 "plots" , "p", 1, "character",
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55 "tximport", "i", 0, "logical",
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56 "txtype", "y", 1, "character",
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57 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)
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58 "fit_type", "t", 1, "integer",
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59 "many_contrasts", "m", 0, "logical",
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60 "outlier_replace_off" , "a", 0, "logical",
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61 "outlier_filter_off" , "b", 0, "logical",
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62 "auto_mean_filter_off", "c", 0, "logical",
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63 "beta_prior_off", "d", 0, "logical"),
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64 byrow=TRUE, ncol=4)
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65 opt <- getopt(spec)
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66
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67 # if help was asked for print a friendly message
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68 # and exit with a non-zero error code
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69 if (!is.null(opt$help)) {
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70 cat(getopt(spec, usage=TRUE))
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71 q(status=1)
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72 }
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73
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74 # enforce the following required arguments
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75 if (is.null(opt$outfile)) {
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76 cat("'outfile' is required\n")
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77 q(status=1)
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78 }
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79 if (is.null(opt$factors)) {
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80 cat("'factors' is required\n")
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81 q(status=1)
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82 }
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83
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84 verbose <- if (is.null(opt$quiet)) {
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85 TRUE
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86 } else {
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87 FALSE
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88 }
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89
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90 if (!is.null(opt$header)) {
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91 hasHeader <- TRUE
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92 } else {
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93 hasHeader <- FALSE
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94 }
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95
6
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96 if (!is.null(opt$tximport)) {
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97 if (is.null(opt$tx2gene)) stop("A transcript-to-gene map or a GTF file is required for tximport")
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98 if (tolower(file_ext(opt$tx2gene)) == "gtf") {
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99 gtfFile <- opt$tx2gene
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100 } else {
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101 gtfFile <- NULL
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102 tx2gene <- read.table(opt$tx2gene, header=FALSE)
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103 }
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104 useTXI <- TRUE
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105 } else {
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106 useTXI <- FALSE
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107 }
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108
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109 suppressPackageStartupMessages({
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110 library("DESeq2")
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111 library("RColorBrewer")
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112 library("gplots")
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113 })
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114
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115 # build or read sample table
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116
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117 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
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118
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119 # switch on if 'factors' was provided:
14
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120 library("rjson")
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121 parser <- newJSONParser()
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122 parser$addData(opt$factors)
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123 factorList <- parser$getObject()
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124 filenames_to_labels <- fromJSON(opt$files_to_labels)
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125 factors <- sapply(factorList, function(x) x[[1]])
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126 primaryFactor <- factors[1]
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127 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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128 labs = unname(unlist(filenames_to_labels[basename(filenamesIn)]))
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129 sampleTable <- data.frame(sample=basename(filenamesIn),
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130 filename=filenamesIn,
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131 row.names=filenamesIn,
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132 stringsAsFactors=FALSE)
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133 for (factor in factorList) {
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134 factorName <- trim(factor[[1]])
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135 sampleTable[[factorName]] <- character(nrow(sampleTable))
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136 lvls <- sapply(factor[[2]], function(x) names(x))
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137 for (i in seq_along(factor[[2]])) {
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138 files <- factor[[2]][[i]][[1]]
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139 sampleTable[files,factorName] <- trim(lvls[i])
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140 }
14
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141 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls)
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142 }
14
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143 rownames(sampleTable) <- labs
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144
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145 primaryFactor <- factors[1]
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146 designFormula <- as.formula(paste("~", paste(rev(factors), collapse=" + ")))
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147
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148 # these are plots which are made once for each analysis
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149 generateGenericPlots <- function(dds, factors) {
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150 library("ggplot2")
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151 library("ggrepel")
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152 library("pheatmap")
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153
6
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154 rld <- rlog(dds)
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155 p <- plotPCA(rld, intgroup=rev(factors))
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156 print(p + geom_text_repel(aes_string(x = "PC1", y = "PC2", label = factor(colnames(dds))), size=3) + geom_point())
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157 dat <- assay(rld)
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158 distsRL <- dist(t(dat))
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159 mat <- as.matrix(distsRL)
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160 colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
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161 pheatmap(mat,
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162 clustering_distance_rows=distsRL,
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163 clustering_distance_cols=distsRL,
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164 col=colors,
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165 main="Sample-to-sample distances")
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166 plotDispEsts(dds, main="Dispersion estimates")
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167 }
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168
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169 # these are plots which can be made for each comparison, e.g.
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170 # once for C vs A and once for B vs A
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171 generateSpecificPlots <- function(res, threshold, title_suffix) {
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172 use <- res$baseMean > threshold
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173 if (sum(!use) == 0) {
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174 h <- hist(res$pvalue, breaks=0:50/50, plot=FALSE)
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175 barplot(height = h$counts,
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176 col = "powderblue", space = 0, xlab="p-values", ylab="frequency",
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177 main=paste("Histogram of p-values for",title_suffix))
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178 text(x = c(0, length(h$counts)), y = 0, label=paste(c(0,1)), adj=c(0.5,1.7), xpd=NA)
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179 } else {
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180 h1 <- hist(res$pvalue[!use], breaks=0:50/50, plot=FALSE)
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181 h2 <- hist(res$pvalue[use], breaks=0:50/50, plot=FALSE)
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182 colori <- c("filtered (low count)"="khaki", "not filtered"="powderblue")
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183 barplot(height = rbind(h1$counts, h2$counts), beside = FALSE,
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184 col = colori, space = 0, xlab="p-values", ylab="frequency",
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185 main=paste("Histogram of p-values for",title_suffix))
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186 text(x = c(0, length(h1$counts)), y = 0, label=paste(c(0,1)), adj=c(0.5,1.7), xpd=NA)
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187 legend("topright", fill=rev(colori), legend=rev(names(colori)), bg="white")
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188 }
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189 plotMA(res, main= paste("MA-plot for",title_suffix), ylim=range(res$log2FoldChange, na.rm=TRUE))
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190 }
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191
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192 if (verbose) {
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193 cat(paste("primary factor:",primaryFactor,"\n"))
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194 if (length(factors) > 1) {
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195 cat(paste("other factors in design:",paste(factors[-length(factors)],collapse=","),"\n"))
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196 }
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197 cat("\n---------------------\n")
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198 }
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199
14
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200 # For JSON input from Galaxy, path is absolute
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201 dir <- ""
6
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202
15
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203 if (!useTXI & hasHeader) {
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204 countfiles <- lapply(as.character(sampleTable$filename), function(x){read.delim(x, row.names=1)})
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205 tbl <- do.call("cbind", countfiles)
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206 colnames(tbl) <- rownames(sampleTable) # take sample ids from header
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207
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208 # check for htseq report lines (from DESeqDataSetFromHTSeqCount function)
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209 oldSpecialNames <- c("no_feature", "ambiguous", "too_low_aQual",
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210 "not_aligned", "alignment_not_unique")
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211 specialRows <- (substr(rownames(tbl), 1, 1) == "_") | rownames(tbl) %in% oldSpecialNames
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212 tbl <- tbl[!specialRows, , drop = FALSE]
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213
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214 dds <- DESeqDataSetFromMatrix(countData = tbl,
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215 colData = sampleTable[,-c(1:2), drop=FALSE],
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216 design = designFormula)
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217 } else if (!useTXI & !hasHeader) {
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218
6
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219 # construct the object from HTSeq files
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220 dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,
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221 directory = dir,
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222 design = designFormula)
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223 labs <- unname(unlist(filenames_to_labels[colnames(dds)]))
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224 colnames(dds) <- labs
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225
6
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226 } else {
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227 # construct the object using tximport
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228 # first need to make the tx2gene table
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229 # this takes ~2-3 minutes using Bioconductor functions
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230 if (!is.null(gtfFile)) {
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231 suppressPackageStartupMessages({
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232 library("GenomicFeatures")
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233 })
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234 txdb <- makeTxDbFromGFF(gtfFile, format="gtf")
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235 k <- keys(txdb, keytype = "GENEID")
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236 df <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
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237 tx2gene <- df[, 2:1] # tx ID, then gene ID
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238 }
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239 library("tximport")
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240 txiFiles <- as.character(sampleTable[,2])
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241 labs <- unname(unlist(filenames_to_labels[sampleTable[,1]]))
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242 names(txiFiles) <- labs
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243 txi <- tximport(txiFiles, type=opt$txtype, tx2gene=tx2gene)
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244 dds <- DESeqDataSetFromTximport(txi,
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245 sampleTable[,3:ncol(sampleTable),drop=FALSE],
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246 designFormula)
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247 }
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248
15
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249 if (verbose) {
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250 cat("DESeq2 run information\n\n")
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251 cat("sample table:\n")
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252 print(sampleTable[,-c(1:2),drop=FALSE])
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253 cat("\ndesign formula:\n")
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254 print(designFormula)
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255 cat("\n\n")
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256 cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
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257 }
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258
6
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259 # optional outlier behavior
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260 if (is.null(opt$outlier_replace_off)) {
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261 minRep <- 7
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262 } else {
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263 minRep <- Inf
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264 if (verbose) cat("outlier replacement off\n")
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265 }
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266 if (is.null(opt$outlier_filter_off)) {
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267 cooksCutoff <- TRUE
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268 } else {
6
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269 cooksCutoff <- FALSE
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270 if (verbose) cat("outlier filtering off\n")
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271 }
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272
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273 # optional automatic mean filtering
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diff changeset
274 if (is.null(opt$auto_mean_filter_off)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
275 independentFiltering <- TRUE
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
276 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
277 independentFiltering <- FALSE
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
278 if (verbose) cat("automatic filtering on the mean off\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
279 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
280
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
281 # shrinkage of LFCs
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
282 if (is.null(opt$beta_prior_off)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
283 betaPrior <- TRUE
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
284 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
285 betaPrior <- FALSE
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
286 if (verbose) cat("beta prior off\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
287 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
288
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
289 # dispersion fit type
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
290 if (is.null(opt$fit_type)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
291 fitType <- "parametric"
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
292 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
293 fitType <- c("parametric","local","mean")[opt$fit_type]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
294 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
295
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
296 if (verbose) cat(paste("using disperion fit type:",fitType,"\n"))
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
297
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
298 # run the analysis
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
299 dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
300
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
301 # create the generic plots and leave the device open
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
302 if (!is.null(opt$plots)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
303 if (verbose) cat("creating plots\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
304 pdf(opt$plots)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
305 generateGenericPlots(dds, factors)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
306 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
307
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
308 n <- nlevels(colData(dds)[[primaryFactor]])
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
309 allLevels <- levels(colData(dds)[[primaryFactor]])
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
310
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
311 if (!is.null(opt$countsfile)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
312 normalizedCounts<-counts(dds,normalized=TRUE)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
313 write.table(normalizedCounts, file=opt$countsfile, sep="\t", col.names=NA, quote=FALSE)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
314 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
315
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
316 if (is.null(opt$many_contrasts)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
317 # only contrast the first and second level of the primary factor
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
318 ref <- allLevels[1]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
319 lvl <- allLevels[2]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
320 res <- results(dds, contrast=c(primaryFactor, lvl, ref),
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
321 cooksCutoff=cooksCutoff,
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
322 independentFiltering=independentFiltering)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
323 if (verbose) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
324 cat("summary of results\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
325 cat(paste0(primaryFactor,": ",lvl," vs ",ref,"\n"))
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
326 print(summary(res))
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
327 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
328 resSorted <- res[order(res$padj),]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
329 outDF <- as.data.frame(resSorted)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
330 outDF$geneID <- rownames(outDF)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
331 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
332 filename <- opt$outfile
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
333 write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
334 if (independentFiltering) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
335 threshold <- unname(attr(res, "filterThreshold"))
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
336 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
337 threshold <- 0
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
338 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
339 title_suffix <- paste0(primaryFactor,": ",lvl," vs ",ref)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
340 if (!is.null(opt$plots)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
341 generateSpecificPlots(res, threshold, title_suffix)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
342 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
343 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
344 # rotate through the possible contrasts of the primary factor
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
345 # write out a sorted table of results with the contrast as a suffix
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
346 # add contrast specific plots to the device
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
347 for (i in seq_len(n-1)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
348 ref <- allLevels[i]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
349 contrastLevels <- allLevels[(i+1):n]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
350 for (lvl in contrastLevels) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
351 res <- results(dds, contrast=c(primaryFactor, lvl, ref),
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
352 cooksCutoff=cooksCutoff,
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
353 independentFiltering=independentFiltering)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
354 resSorted <- res[order(res$padj),]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
355 outDF <- as.data.frame(resSorted)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
356 outDF$geneID <- rownames(outDF)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
357 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
358 filename <- paste0(opt$outfile,".",primaryFactor,"_",lvl,"_vs_",ref)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
359 write.table(outDF, file=filename, sep="\t", quote=FALSE, row.names=FALSE, col.names=FALSE)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
360 if (independentFiltering) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
361 threshold <- unname(attr(res, "filterThreshold"))
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
362 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
363 threshold <- 0
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
364 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
365 title_suffix <- paste0(primaryFactor,": ",lvl," vs ",ref)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
366 if (!is.null(opt$plots)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
367 generateSpecificPlots(res, threshold, title_suffix)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
368 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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369 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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370 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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371 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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373 # close the plot device
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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374 if (!is.null(opt$plots)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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375 cat("closing plot device\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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376 dev.off()
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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377 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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378
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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379 cat("Session information:\n\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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380
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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381 sessionInfo()
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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382