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annotate deseq2.R @ 24:71bacea10eee draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
author iuc
date Sat, 29 Feb 2020 17:08:08 -0500
parents a6fc9228e1a0
children de44f8eff84a
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1 #!/usr/bin/env Rscript
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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 "cores", "s", 0, "integer",
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50 "batch_factors", "w", 1, "character",
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51 "outfile", "o", 1, "character",
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52 "countsfile", "n", 1, "character",
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53 "rlogfile", "r", 1, "character",
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54 "vstfile", "v", 1, "character",
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55 "header", "H", 0, "logical",
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56 "factors", "f", 1, "character",
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57 "files_to_labels", "l", 1, "character",
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58 "plots" , "p", 1, "character",
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59 "tximport", "i", 0, "logical",
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60 "txtype", "y", 1, "character",
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61 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF/GFF3 file
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62 "esf", "e", 1, "character",
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63 "fit_type", "t", 1, "integer",
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64 "many_contrasts", "m", 0, "logical",
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65 "outlier_replace_off" , "a", 0, "logical",
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66 "outlier_filter_off" , "b", 0, "logical",
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67 "auto_mean_filter_off", "c", 0, "logical",
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68 "beta_prior_off", "d", 0, "logical"),
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69 byrow=TRUE, ncol=4)
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70 opt <- getopt(spec)
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72 # if help was asked for print a friendly message
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73 # and exit with a non-zero error code
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74 if (!is.null(opt$help)) {
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75 cat(getopt(spec, usage=TRUE))
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76 q(status=1)
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77 }
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78
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79 # enforce the following required arguments
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80 if (is.null(opt$outfile)) {
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81 cat("'outfile' is required\n")
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82 q(status=1)
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83 }
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84 if (is.null(opt$factors)) {
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85 cat("'factors' is required\n")
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86 q(status=1)
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87 }
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88
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89 verbose <- if (is.null(opt$quiet)) {
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90 TRUE
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91 } else {
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92 FALSE
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93 }
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94
17
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95 source_local <- function(fname){
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96 argv <- commandArgs(trailingOnly = FALSE)
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97 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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98 source(paste(base_dir, fname, sep="/"))
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99 }
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100
17
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101 source_local('get_deseq_dataset.R')
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102
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103 suppressPackageStartupMessages({
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104 library("DESeq2")
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105 library("RColorBrewer")
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106 library("gplots")
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107 })
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108
21
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109 if (opt$cores > 1) {
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110 library("BiocParallel")
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111 register(MulticoreParam(opt$cores))
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112 parallel = TRUE
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113 } else {
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114 parallel = FALSE
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115 }
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116
6
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117 # build or read sample table
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118
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119 trim <- function (x) gsub("^\\s+|\\s+$", "", x)
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120
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121 # switch on if 'factors' was provided:
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122 library("rjson")
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123 parser <- newJSONParser()
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124 parser$addData(opt$factors)
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125 factorList <- parser$getObject()
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126 filenames_to_labels <- fromJSON(opt$files_to_labels)
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127 factors <- sapply(factorList, function(x) x[[1]])
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128 primaryFactor <- factors[1]
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129 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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130 labs = unname(unlist(filenames_to_labels[basename(filenamesIn)]))
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131 sampleTable <- data.frame(sample=basename(filenamesIn),
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132 filename=filenamesIn,
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133 row.names=filenamesIn,
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134 stringsAsFactors=FALSE)
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135 for (factor in factorList) {
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136 factorName <- trim(factor[[1]])
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137 sampleTable[[factorName]] <- character(nrow(sampleTable))
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138 lvls <- sapply(factor[[2]], function(x) names(x))
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139 for (i in seq_along(factor[[2]])) {
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140 files <- factor[[2]][[i]][[1]]
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141 sampleTable[files,factorName] <- trim(lvls[i])
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142 }
14
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143 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls)
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144 }
14
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145 rownames(sampleTable) <- labs
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146
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147 primaryFactor <- factors[1]
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148 designFormula <- as.formula(paste("~", paste(rev(factors), collapse=" + ")))
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149
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150 # these are plots which are made once for each analysis
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151 generateGenericPlots <- function(dds, factors) {
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152 library("ggplot2")
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153 library("ggrepel")
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154 library("pheatmap")
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155
6
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156 rld <- rlog(dds)
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157 p <- plotPCA(rld, intgroup=rev(factors))
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158 print(p + geom_text_repel(aes_string(x = "PC1", y = "PC2", label = factor(colnames(dds))), size=3) + geom_point())
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159 dat <- assay(rld)
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160 distsRL <- dist(t(dat))
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161 mat <- as.matrix(distsRL)
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162 colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
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163 pheatmap(mat,
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164 clustering_distance_rows=distsRL,
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165 clustering_distance_cols=distsRL,
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166 col=colors,
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167 main="Sample-to-sample distances")
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168 plotDispEsts(dds, main="Dispersion estimates")
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169 }
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170
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171 # these are plots which can be made for each comparison, e.g.
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172 # once for C vs A and once for B vs A
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173 generateSpecificPlots <- function(res, threshold, title_suffix) {
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174 use <- res$baseMean > threshold
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175 if (sum(!use) == 0) {
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176 h <- hist(res$pvalue, breaks=0:50/50, plot=FALSE)
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177 barplot(height = h$counts,
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178 col = "powderblue", space = 0, xlab="p-values", ylab="frequency",
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179 main=paste("Histogram of p-values for",title_suffix))
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180 text(x = c(0, length(h$counts)), y = 0, label=paste(c(0,1)), adj=c(0.5,1.7), xpd=NA)
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181 } else {
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182 h1 <- hist(res$pvalue[!use], breaks=0:50/50, plot=FALSE)
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183 h2 <- hist(res$pvalue[use], breaks=0:50/50, plot=FALSE)
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184 colori <- c("filtered (low count)"="khaki", "not filtered"="powderblue")
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185 barplot(height = rbind(h1$counts, h2$counts), beside = FALSE,
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186 col = colori, space = 0, xlab="p-values", ylab="frequency",
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187 main=paste("Histogram of p-values for",title_suffix))
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188 text(x = c(0, length(h1$counts)), y = 0, label=paste(c(0,1)), adj=c(0.5,1.7), xpd=NA)
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189 legend("topright", fill=rev(colori), legend=rev(names(colori)), bg="white")
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190 }
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191 plotMA(res, main= paste("MA-plot for",title_suffix), ylim=range(res$log2FoldChange, na.rm=TRUE))
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192 }
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193
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194 if (verbose) {
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195 cat(paste("primary factor:",primaryFactor,"\n"))
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196 if (length(factors) > 1) {
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197 cat(paste("other factors in design:",paste(factors[-length(factors)],collapse=","),"\n"))
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198 }
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199 cat("\n---------------------\n")
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200 }
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201
17
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202 dds <- get_deseq_dataset(sampleTable, header=opt$header, designFormula=designFormula, tximport=opt$tximport, txtype=opt$txtype, tx2gene=opt$tx2gene)
18
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203 # estimate size factors for the chosen method
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204 if(!is.null(opt$esf)){
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205 dds <- estimateSizeFactors(dds, type=opt$esf)
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206 }
17
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207 apply_batch_factors <- function (dds, batch_factors) {
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208 rownames(batch_factors) <- batch_factors$identifier
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209 batch_factors <- subset(batch_factors, select = -c(identifier, condition))
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210 dds_samples <- colnames(dds)
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211 batch_samples <- rownames(batch_factors)
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212 if (!setequal(batch_samples, dds_samples)) {
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213 stop("Batch factor names don't correspond to input sample names, check input files")
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214 }
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215 dds_data <- colData(dds)
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216 # Merge dds_data with batch_factors using indexes, which are sample names
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217 # Set sort to False, which maintains the order in dds_data
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218 reordered_batch <- merge(dds_data, batch_factors, by.x = 0, by.y = 0, sort=F)
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219 batch_factors <- reordered_batch[, ncol(dds_data):ncol(reordered_batch)]
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220 for (factor in colnames(batch_factors)) {
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221 dds[[factor]] <- batch_factors[[factor]]
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222 }
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223 colnames(dds) <- reordered_batch[,1]
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224 return(dds)
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225 }
15
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226
17
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227 if (!is.null(opt$batch_factors)) {
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228 batch_factors <- read.table(opt$batch_factors, sep="\t", header=T)
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229 dds <- apply_batch_factors(dds = dds, batch_factors = batch_factors)
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230 batch_design <- colnames(batch_factors)[-c(1,2)]
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231 designFormula <- as.formula(paste("~", paste(c(batch_design, rev(factors)), collapse=" + ")))
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232 design(dds) <- designFormula
6
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233 }
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234
15
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235 if (verbose) {
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236 cat("DESeq2 run information\n\n")
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237 cat("sample table:\n")
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238 print(sampleTable[,-c(1:2),drop=FALSE])
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239 cat("\ndesign formula:\n")
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240 print(designFormula)
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241 cat("\n\n")
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242 cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
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243 }
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244
6
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245 # optional outlier behavior
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246 if (is.null(opt$outlier_replace_off)) {
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247 minRep <- 7
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248 } else {
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249 minRep <- Inf
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250 if (verbose) cat("outlier replacement off\n")
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251 }
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252 if (is.null(opt$outlier_filter_off)) {
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253 cooksCutoff <- TRUE
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254 } else {
6
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255 cooksCutoff <- FALSE
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256 if (verbose) cat("outlier filtering off\n")
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257 }
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258
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259 # optional automatic mean filtering
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260 if (is.null(opt$auto_mean_filter_off)) {
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261 independentFiltering <- TRUE
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262 } else {
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263 independentFiltering <- FALSE
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264 if (verbose) cat("automatic filtering on the mean off\n")
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265 }
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266
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267 # shrinkage of LFCs
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268 if (is.null(opt$beta_prior_off)) {
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269 betaPrior <- TRUE
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270 } else {
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271 betaPrior <- FALSE
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272 if (verbose) cat("beta prior off\n")
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273 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
274
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
275 # dispersion fit type
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
276 if (is.null(opt$fit_type)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
277 fitType <- "parametric"
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
278 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
279 fitType <- c("parametric","local","mean")[opt$fit_type]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
280 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
281
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
282 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
283
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
284 # run the analysis
21
a6fc9228e1a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 05bc13637dc9f8e523bc72844ff6eb0794f98ad3
iuc
parents: 19
diff changeset
285 dds <- DESeq(dds, fitType=fitType, betaPrior=betaPrior, minReplicatesForReplace=minRep, parallel=parallel)
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
286
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
287 # 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
288 if (!is.null(opt$plots)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
289 if (verbose) cat("creating plots\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
290 pdf(opt$plots)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
291 generateGenericPlots(dds, factors)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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292 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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293
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
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294 n <- nlevels(colData(dds)[[primaryFactor]])
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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295 allLevels <- levels(colData(dds)[[primaryFactor]])
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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296
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
297 if (!is.null(opt$countsfile)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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298 normalizedCounts<-counts(dds,normalized=TRUE)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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299 write.table(normalizedCounts, file=opt$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:
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300 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
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301
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
302 if (!is.null(opt$rlogfile)) {
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
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diff changeset
303 rLogNormalized <-rlogTransformation(dds)
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
304 rLogNormalizedMat <- assay(rLogNormalized)
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
305 write.table(rLogNormalizedMat, file=opt$rlogfile, sep="\t", col.names=NA, quote=FALSE)
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
306 }
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
307
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
308 if (!is.null(opt$vstfile)) {
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
309 vstNormalized<-varianceStabilizingTransformation(dds)
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
310 vstNormalizedMat <- assay(vstNormalized)
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
311 write.table(vstNormalizedMat, file=opt$vstfile, sep="\t", col.names=NA, quote=FALSE)
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
312 }
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
313
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
314
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
315 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
316 # 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
317 ref <- allLevels[1]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
318 lvl <- allLevels[2]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
319 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
320 cooksCutoff=cooksCutoff,
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
321 independentFiltering=independentFiltering)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
322 if (verbose) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
323 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
324 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
325 print(summary(res))
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
326 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
327 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
328 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
329 outDF$geneID <- rownames(outDF)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
330 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
331 filename <- opt$outfile
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
332 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
333 if (independentFiltering) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
334 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
335 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
336 threshold <- 0
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
337 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
338 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
339 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
340 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
341 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
342 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
343 # 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
344 # 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
345 # 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
346 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
347 ref <- allLevels[i]
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
348 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
349 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
350 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
351 cooksCutoff=cooksCutoff,
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
352 independentFiltering=independentFiltering)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
353 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
354 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
355 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
356 outDF <- outDF[,c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
24
71bacea10eee "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 29f5fd6ec10122f7b241c8d36d648b105ed4275a"
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parents: 21
diff changeset
357 filename <- paste0(primaryFactor,"_",lvl,"_vs_",ref)
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
358 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
359 if (independentFiltering) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
360 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
361 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
362 threshold <- 0
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
363 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
364 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
365 if (!is.null(opt$plots)) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
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366 generateSpecificPlots(res, threshold, title_suffix)
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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367 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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368 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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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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372 # close the plot device
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
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373 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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374 cat("closing plot device\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
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375 dev.off()
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
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376 }
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 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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379
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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380 sessionInfo()
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
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381