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annotate deseq2.R @ 31:9a882d108833 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
author iuc
date Tue, 18 Jul 2023 14:58:52 +0000
parents 8fe98f7094de
children
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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 = FALSE, error = function() {
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35 cat(geterrmessage(), file = stderr())
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36 q("no", 1, FALSE)
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37 })
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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 "sizefactorsfile", "F", 1, "character",
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54 "rlogfile", "r", 1, "character",
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55 "vstfile", "v", 1, "character",
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56 "header", "H", 0, "logical",
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57 "factors", "f", 1, "character",
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58 "files_to_labels", "l", 1, "character",
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59 "plots", "p", 1, "character",
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60 "tximport", "i", 0, "logical",
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61 "txtype", "y", 1, "character",
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62 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF/GFF3 file
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63 "esf", "e", 1, "character",
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64 "fit_type", "t", 1, "integer",
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65 "many_contrasts", "m", 0, "logical",
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66 "outlier_replace_off", "a", 0, "logical",
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67 "outlier_filter_off", "b", 0, "logical",
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68 "auto_mean_filter_off", "c", 0, "logical",
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69 "use_beta_priors", "d", 0, "logical",
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70 "alpha_ma", "A", 1, "numeric",
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71 "prefilter", "P", 0, "logical",
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72 "prefilter_value", "V", 1, "numeric"
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73 ), byrow = TRUE, ncol = 4)
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74 opt <- getopt(spec)
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75
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76 # if help was asked for print a friendly message
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77 # and exit with a non-zero error code
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78 if (!is.null(opt$help)) {
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79 cat(getopt(spec, usage = TRUE))
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80 q(status = 1)
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81 }
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83 # enforce the following required arguments
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84 if (is.null(opt$outfile)) {
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85 cat("'outfile' is required\n")
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86 q(status = 1)
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87 }
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88 if (is.null(opt$factors)) {
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89 cat("'factors' is required\n")
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90 q(status = 1)
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91 }
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92
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93 verbose <- is.null(opt$quiet)
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94
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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
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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
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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
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117 # build or read sample table
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118
25
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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$factors)
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125 factor_list <- parser$getObject()
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126 filenames_to_labels <- fromJSON(opt$files_to_labels)
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127 factors <- sapply(factor_list, function(x) x[[1]])
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128 primary_factor <- factors[1]
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129 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
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130 labs <- unname(unlist(filenames_to_labels[basename(filenames_in)]))
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131 sample_table <- data.frame(
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132 sample = basename(filenames_in),
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133 filename = filenames_in,
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134 row.names = filenames_in,
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135 stringsAsFactors = FALSE
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136 )
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137 for (factor in factor_list) {
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138 factor_name <- trim(factor[[1]])
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139 sample_table[[factor_name]] <- character(nrow(sample_table))
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140 lvls <- sapply(factor[[2]], function(x) names(x))
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141 for (i in seq_along(factor[[2]])) {
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142 files <- factor[[2]][[i]][[1]]
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143 sample_table[files, factor_name] <- trim(lvls[i])
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144 }
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145 sample_table[[factor_name]] <- factor(sample_table[[factor_name]], levels = lvls)
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146 }
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147 rownames(sample_table) <- labs
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148
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149 design_formula <- as.formula(paste("~", paste(rev(factors), collapse = " + ")))
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150
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151 # these are plots which are made once for each analysis
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152 generate_generic_plots <- function(dds, factors) {
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153 library("ggplot2")
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154 library("ggrepel")
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155 library("pheatmap")
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156
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157 rld <- rlog(dds)
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158 p <- plotPCA(rld, intgroup = rev(factors))
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159 print(p + geom_text_repel(aes_string(x = "PC1", y = "PC2", label = factor(colnames(dds))), size = 3) + geom_point())
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160 dat <- assay(rld)
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161 dists_rl <- dist(t(dat))
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162 mat <- as.matrix(dists_rl)
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163 colors <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)
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164 pheatmap(
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165 mat,
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166 clustering_distance_rows = dists_rl,
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167 clustering_distance_cols = dists_rl,
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168 col = colors,
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169 main = "Sample-to-sample distances"
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170 )
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171 plotDispEsts(dds, main = "Dispersion estimates")
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172 }
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173
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174 # these are plots which can be made for each comparison, e.g.
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175 # once for C vs A and once for B vs A
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176 generate_specific_plots <- function(res, threshold, title_suffix) {
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177 use <- res$baseMean > threshold
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178 if (sum(!use) == 0) {
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179 h <- hist(res$pvalue, breaks = 0:50 / 50, plot = FALSE)
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180 barplot(
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181 height = h$counts,
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182 col = "powderblue",
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183 space = 0,
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184 xlab = "p-values",
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185 ylab = "frequency",
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186 main = paste("Histogram of p-values for", title_suffix)
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187 )
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188 text(x = c(0, length(h$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA)
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189 } else {
25
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190 h1 <- hist(res$pvalue[!use], breaks = 0:50 / 50, plot = FALSE)
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191 h2 <- hist(res$pvalue[use], breaks = 0:50 / 50, plot = FALSE)
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192 colori <- c("filtered (low count)" = "khaki", "not filtered" = "powderblue")
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193 barplot(
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194 height = rbind(h1$counts, h2$counts),
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195 beside = FALSE,
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196 col = colori,
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197 space = 0,
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198 xlab = "p-values",
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199 ylab = "frequency",
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200 main = paste("Histogram of p-values for", title_suffix)
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201 )
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202 text(x = c(0, length(h1$counts)), y = 0, label = paste(c(0, 1)), adj = c(0.5, 1.7), xpd = NA)
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203 legend("topright", fill = rev(colori), legend = rev(names(colori)), bg = "white")
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204 }
27
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205 plotMA(res, main = paste("MA-plot for", title_suffix), ylim = range(res$log2FoldChange, na.rm = TRUE), alpha = opt$alpha_ma)
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206 }
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207
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208 if (verbose) {
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209 cat(paste("primary factor:", primary_factor, "\n"))
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210 if (length(factors) > 1) {
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211 cat(paste("other factors in design:", paste(factors[-length(factors)], collapse = ","), "\n"))
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212 }
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213 cat("\n---------------------\n")
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214 }
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215
25
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216 dds <- get_deseq_dataset(sample_table, header = opt$header, design_formula = design_formula, tximport = opt$tximport, txtype = opt$txtype, tx2gene = opt$tx2gene)
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217
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218 # use/estimate size factors with the chosen method
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219 if (!is.null(opt$esf)) {
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220 if (opt$esf %in% list("ratio", "poscounts", "iterate")) {
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221 cat("Calculating size factors de novo\n")
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222 dds <- estimateSizeFactors(dds, type = opt$esf)
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223 } else {
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224 sf_table <- read.table(opt$esf)
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225 # Sort the provided size factors just in case the order differs from the input file order.
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226 merged_table <- merge(sample_table, sf_table, by.x = 0, by.y = 1, sort = FALSE)
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227 sf_values <- as.numeric(unlist(merged_table[5]))
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228 "sizeFactors"(dds) <- sf_values
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229
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230 cat("Using user-provided size factors:\n")
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231 print(sf_values)
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232 }
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233 } else {
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234 cat("No size factor was used\n")
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235 }
29
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236
31
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237
29
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238 # estimate size factors for each sample
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239 # - https://support.bioconductor.org/p/97676/
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240 if (!is.null(opt$sizefactorsfile)) {
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241 nm <- assays(dds)[["avgTxLength"]]
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242 if (!is.null(nm)) {
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243 ## Recommended: takes into account tximport data
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244 cat("\nsize factors for samples: taking tximport data into account\n")
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245 size_factors <- estimateSizeFactorsForMatrix(counts(dds) / nm)
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246 } else {
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247 norm_factors <- normalizationFactors(dds)
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248 if (!is.null(norm_factors)) {
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249 ## In practice, gives same results as above.
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250 cat("\nsize factors for samples: no tximport data, using derived normalization factors\n")
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251 size_factors <- estimateSizeFactorsForMatrix(norm_factors)
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252 } else {
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253 ## If we have no other information, estimate from raw.
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254 cat("\nsize factors for samples: no tximport data, no normalization factors, estimating from raw data\n")
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255 size_factors <- estimateSizeFactorsForMatrix(counts(dds))
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256 }
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257 }
30
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258 write.table(size_factors, file = opt$sizefactorsfile, sep = "\t", col.names = FALSE, quote = FALSE)
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259 }
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260
25
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261 apply_batch_factors <- function(dds, batch_factors) {
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262 rownames(batch_factors) <- batch_factors$identifier
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263 batch_factors <- subset(batch_factors, select = -c(identifier, condition))
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264 dds_samples <- colnames(dds)
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265 batch_samples <- rownames(batch_factors)
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266 if (!setequal(batch_samples, dds_samples)) {
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267 stop("Batch factor names don't correspond to input sample names, check input files")
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268 }
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269 dds_data <- colData(dds)
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270 # Merge dds_data with batch_factors using indexes, which are sample names
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271 # Set sort to False, which maintains the order in dds_data
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272 reordered_batch <- merge(dds_data, batch_factors, by.x = 0, by.y = 0, sort = FALSE)
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273 batch_factors <- reordered_batch[, ncol(dds_data):ncol(reordered_batch)]
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274 for (factor in colnames(batch_factors)) {
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275 dds[[factor]] <- batch_factors[[factor]]
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276 }
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277 colnames(dds) <- reordered_batch[, 1]
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278 return(dds)
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279 }
15
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280
17
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281 if (!is.null(opt$batch_factors)) {
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282 batch_factors <- read.table(opt$batch_factors, sep = "\t", header = TRUE)
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283 dds <- apply_batch_factors(dds = dds, batch_factors = batch_factors)
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284 batch_design <- colnames(batch_factors)[-c(1, 2)]
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285 design_formula <- as.formula(paste("~", paste(c(batch_design, rev(factors)), collapse = " + ")))
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286 design(dds) <- design_formula
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287 }
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288
15
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289 if (verbose) {
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290 cat("DESeq2 run information\n\n")
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291 cat("sample table:\n")
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292 print(sample_table[, -c(1:2), drop = FALSE])
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293 cat("\ndesign formula:\n")
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294 print(design_formula)
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295 cat("\n\n")
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296 cat(paste(ncol(dds), "samples with counts over", nrow(dds), "genes\n"))
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297 }
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298
30
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299 # minimal pre-filtering
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300 if (!is.null(opt$prefilter)) {
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301 keep <- rowSums(counts(dds)) >= opt$prefilter_value
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302 dds <- dds[keep, ]
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303 }
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304
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305 # optional outlier behavior
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306 if (is.null(opt$outlier_replace_off)) {
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307 min_rep <- 7
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308 } else {
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309 min_rep <- Inf
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310 if (verbose) cat("outlier replacement off\n")
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311 }
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312 if (is.null(opt$outlier_filter_off)) {
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313 cooks_cutoff <- TRUE
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314 } else {
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315 cooks_cutoff <- FALSE
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316 if (verbose) cat("outlier filtering off\n")
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317 }
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318
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319 # optional automatic mean filtering
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320 if (is.null(opt$auto_mean_filter_off)) {
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321 independent_filtering <- TRUE
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322 } else {
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323 independent_filtering <- FALSE
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324 if (verbose) cat("automatic filtering on the mean off\n")
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325 }
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326
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327 # shrinkage of LFCs
31
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328 if (is.null(opt$use_beta_priors)) {
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329 beta_prior <- FALSE
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330 if (verbose)
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331 cat("Applied default - beta prior off\n")
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332 } else {
31
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333 beta_prior <- opt$use_beta_priors
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334 }
31
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335 sprintf("use_beta_prior is set to %s", beta_prior)
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336
6
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337
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338 # dispersion fit type
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339 if (is.null(opt$fit_type)) {
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340 fit_type <- "parametric"
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341 } else {
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342 fit_type <- c("parametric", "local", "mean")[opt$fit_type]
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343 }
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344
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345 if (verbose) cat(paste("using disperion fit type:", fit_type, "\n"))
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346
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347 # run the analysis
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348 dds <- DESeq(dds, fitType = fit_type, betaPrior = beta_prior, minReplicatesForReplace = min_rep, parallel = parallel)
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349
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350 # create the generic plots and leave the device open
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351 if (!is.null(opt$plots)) {
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352 if (verbose) cat("creating plots\n")
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353 pdf(opt$plots)
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354 generate_generic_plots(dds, factors)
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355 }
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356
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357 n <- nlevels(colData(dds)[[primary_factor]])
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358 all_levels <- levels(colData(dds)[[primary_factor]])
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359
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360 if (!is.null(opt$countsfile)) {
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de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
361 normalized_counts <- counts(dds, normalized = TRUE)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
362 write.table(normalized_counts, file = opt$countsfile, sep = "\t", col.names = NA, quote = FALSE)
6
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
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
365 if (!is.null(opt$rlogfile)) {
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
366 rlog_normalized <- rlogTransformation(dds)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
367 rlog_normalized_mat <- assay(rlog_normalized)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
368 write.table(rlog_normalized_mat, file = opt$rlogfile, sep = "\t", col.names = NA, quote = FALSE)
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
369 }
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
370
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
371 if (!is.null(opt$vstfile)) {
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
372 vst_normalized <- varianceStabilizingTransformation(dds)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
373 vst_normalized_mat <- assay(vst_normalized)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
374 write.table(vst_normalized_mat, file = opt$vstfile, sep = "\t", col.names = NA, quote = FALSE)
18
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
375 }
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
376
3bf1b3ec1ddf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 448dccb0c02aba00d8301247b0f0f406ab3d4fa2
iuc
parents: 17
diff changeset
377
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
378 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
379 # only contrast the first and second level of the primary factor
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
380 ref <- all_levels[1]
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
381 lvl <- all_levels[2]
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
382 res <- results(
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
383 dds,
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
384 contrast = c(primary_factor, lvl, ref),
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
385 cooksCutoff = cooks_cutoff,
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
386 independentFiltering = independent_filtering
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
387 )
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
388 if (verbose) {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
389 cat("summary of results\n")
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
390 cat(paste0(primary_factor, ": ", lvl, " vs ", ref, "\n"))
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
391 print(summary(res))
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
392 }
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
393 res_sorted <- res[order(res$padj), ]
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
394 out_df <- as.data.frame(res_sorted)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
395 out_df$geneID <- rownames(out_df) # nolint
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
396 out_df <- out_df[, c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
397 filename <- opt$outfile
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
398 write.table(out_df, file = filename, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
399 if (independent_filtering) {
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
400 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
401 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
402 threshold <- 0
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
403 }
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
404 title_suffix <- paste0(primary_factor, ": ", 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
405 if (!is.null(opt$plots)) {
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
406 generate_specific_plots(res, threshold, title_suffix)
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
407 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
408 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
409 # 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
410 # 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
411 # add contrast specific plots to the device
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
412 for (i in seq_len(n - 1)) {
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
413 ref <- all_levels[i]
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
414 contrast_levels <- all_levels[(i + 1):n]
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
415 for (lvl in contrast_levels) {
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
416 res <- results(
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
417 dds,
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
418 contrast = c(primary_factor, lvl, ref),
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
419 cooksCutoff = cooks_cutoff,
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
420 independentFiltering = independent_filtering
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
421 )
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
422 res_sorted <- res[order(res$padj), ]
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
423 out_df <- as.data.frame(res_sorted)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
424 out_df$geneID <- rownames(out_df) # nolint
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
425 out_df <- out_df[, c("geneID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj")]
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
426 filename <- paste0(primary_factor, "_", lvl, "_vs_", ref)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
427 write.table(out_df, file = filename, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
428 if (independent_filtering) {
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
429 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
430 } else {
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
431 threshold <- 0
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
432 }
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
433 title_suffix <- paste0(primary_factor, ": ", 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
434 if (!is.null(opt$plots)) {
25
de44f8eff84a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
iuc
parents: 24
diff changeset
435 generate_specific_plots(res, threshold, title_suffix)
6
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
436 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
437 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
438 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
439 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
440
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
441 # close the plot device
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
442 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
443 cat("closing plot device\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
444 dev.off()
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
445 }
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
446
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
447 cat("Session information:\n\n")
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
448
4939397c4706 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 3bc8d91ee546682ef8e9303bd1044bb14cf21b07
iuc
parents:
diff changeset
449 sessionInfo()