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annotate edger.R @ 15:119f41ec0ada draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212
author iuc
date Wed, 15 Oct 2025 10:24:03 +0000
parents c5fa04118f83
children 09965c918573
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1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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1 # This tool takes in a matrix of feature counts as well as gene annotations and
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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2 # outputs a table of top expressions as well as various plots for differential
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3 # expression analysis
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4 #
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5 # ARGS: htmlPath", "R", 1, "character" -Path to html file linking to other outputs
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6 # outPath", "o", 1, "character" -Path to folder to write all output to
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7 # filesPath", "j", 2, "character" -JSON list object if multiple files input
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8 # matrixPath", "m", 2, "character" -Path to count matrix
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9 # factFile", "f", 2, "character" -Path to factor information file
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10 # factInput", "i", 2, "character" -String containing factors if manually input
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11 # formula", "F", 2, "character". -String containing a formula to override default use of factInput
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12 # annoPath", "a", 2, "character" -Path to input containing gene annotations
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13 # contrastData", "C", 1, "character" -String containing contrasts of interest
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14 # cpmReq", "c", 2, "double" -Float specifying cpm requirement
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15 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement
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16 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement
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17 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output
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18 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output
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19 # lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement
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20 # pValReq", "p", 1, "double" -Float specifying the p-value requirement
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21 # pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method
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22 # normOpt", "n", 1, "character" -String specifying type of normalisation used
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23 # robOpt", "b", 0, "logical" -String specifying if robust options should be used
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24 # lrtOpt", "t", 0, "logical" -String specifying whether to perform LRT test instead
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25 #
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26 # OUT:
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27 # MDS Plot
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28 # BCV Plot
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29 # QL Plot
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30 # MD Plot
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31 # Expression Table
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32 # HTML file linking to the ouputs
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33 # Optional:
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34 # Normalised counts Table
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35 # RData file
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36 #
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37 # Author: Shian Su - registertonysu@gmail.com - Jan 2014
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38 # Modified by: Maria Doyle - Oct 2017 (some code taken from the DESeq2 wrapper)
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40 # Record starting time
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41 time_start <- as.character(Sys.time())
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43 # setup R error handling to go to stderr
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44 options(show.error.messages = FALSE, error = function() {
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45 cat(geterrmessage(), file = stderr())
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46 q("no", 1, FALSE)
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47 })
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48
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49 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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50 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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51
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52 # Load all required libraries
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53 library(methods, quietly = TRUE, warn.conflicts = FALSE)
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54 library(statmod, quietly = TRUE, warn.conflicts = FALSE)
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55 library(splines, quietly = TRUE, warn.conflicts = FALSE)
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56 library(edgeR, quietly = TRUE, warn.conflicts = FALSE)
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57 library(limma, quietly = TRUE, warn.conflicts = FALSE)
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58 library(scales, quietly = TRUE, warn.conflicts = FALSE)
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59 library(getopt, quietly = TRUE, warn.conflicts = FALSE)
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60
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61 ################################################################################
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62 ### Function Delcaration
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63 ################################################################################
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64 # Function to sanitise contrast equations so there are no whitespaces
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65 # surrounding the arithmetic operators, leading or trailing whitespace
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66 sanitise_equation <- function(equation) {
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67 equation <- gsub(" *[+] *", "+", equation)
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68 equation <- gsub(" *[-] *", "-", equation)
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69 equation <- gsub(" *[/] *", "/", equation)
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70 equation <- gsub(" *[*] *", "*", equation)
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71 equation <- gsub("^\\s+|\\s+$", "", equation)
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72 return(equation)
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73 }
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75 # Function to sanitise group information
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76 sanitise_groups <- function(string) {
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77 string <- gsub(" *[,] *", ",", string)
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78 string <- gsub("^\\s+|\\s+$", "", string)
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79 return(string)
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80 }
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81
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82 # Function to change periods to whitespace in a string
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83 unmake_names <- function(string) {
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84 string <- gsub(".", " ", string, fixed = TRUE)
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85 return(string)
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86 }
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87
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88 # Sanitise file base names coming from factors or contrasts
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89 sanitise_basename <- function(string) {
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90 string <- gsub("[/^]", "_", string)
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91 return(string)
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92 }
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93
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94 # Generate output folder and paths
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95 make_out <- function(filename) {
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96 return(paste0(out_path, "/", filename))
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97 }
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98
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99 # Generating design information
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100 paste_listname <- function(string) {
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101 return(paste0("factors$", string))
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102 }
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103
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104 # Create cata function: default path set, default seperator empty and appending
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105 # true by default (Ripped straight from the cat function with altered argument
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106 # defaults)
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107 cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL,
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108 append = TRUE) {
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109 if (is.character(file)) {
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110 if (file == "") {
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111 file <- stdout()
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112 } else if (substring(file, 1L, 1L) == "|") {
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113 file <- pipe(substring(file, 2L), "w")
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114 on.exit(close(file))
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115 } else {
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116 file <- file(file, ifelse(append, "a", "w"))
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117 on.exit(close(file))
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118 }
0
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119 }
14
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120 .Internal(cat(list(...), file, sep, fill, labels, append))
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121 }
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122
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123 # Function to write code for html head and title
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124 html_head <- function(title) {
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125 cata("<head>\n")
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126 cata("<title>", title, "</title>\n")
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127 cata("</head>\n")
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128 }
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129
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130 # Function to write code for html links
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131 html_link <- function(address, label = address) {
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132 cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n")
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133 }
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134
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135 # Function to write code for html images
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136 html_image <- function(source, label = source, height = 600, width = 600) {
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137 cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height)
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138 cata("\" width=\"", width, "\"/>\n")
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139 }
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140
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141 # Function to write code for html list items
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142 list_item <- function(...) {
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143 cata("<li>", ..., "</li>\n")
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144 }
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145
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146 table_item <- function(...) {
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147 cata("<td>", ..., "</td>\n")
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148 }
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149
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150 table_head_item <- function(...) {
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151 cata("<th>", ..., "</th>\n")
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152 }
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153
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154 ################################################################################
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155 ### Input Processing
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156 ################################################################################
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157
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158 # Collect arguments from command line
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159 args <- commandArgs(trailingOnly = TRUE)
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160
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161 # Get options, using the spec as defined by the enclosed list.
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162 # Read the options from the default: commandArgs(TRUE).
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163 spec <- matrix(
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164 c(
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165 "htmlPath", "R", 1, "character",
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166 "outPath", "o", 1, "character",
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167 "filesPath", "j", 2, "character",
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168 "matrixPath", "m", 2, "character",
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169 "factFile", "f", 2, "character",
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170 "formula", "F", 2, "character",
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171 "factInput", "i", 2, "character",
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172 "annoPath", "a", 2, "character",
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173 "contrastData", "C", 1, "character",
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174 "cpmReq", "c", 1, "double",
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175 "totReq", "y", 0, "logical",
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176 "cntReq", "z", 1, "integer",
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177 "sampleReq", "s", 1, "integer",
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178 "normCounts", "x", 0, "logical",
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179 "rdaOpt", "r", 0, "logical",
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180 "lfcReq", "l", 1, "double",
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181 "pValReq", "p", 1, "double",
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182 "pAdjOpt", "d", 1, "character",
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183 "normOpt", "n", 1, "character",
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184 "robOpt", "b", 0, "logical",
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185 "lrtOpt", "t", 0, "logical"
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186 ),
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187 byrow = TRUE, ncol = 4
8
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188 )
0
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189 opt <- getopt(spec)
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190
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191
12
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192 if (is.null(opt$matrixPath) && is.null(opt$filesPath)) {
14
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193 cat("A counts matrix (or a set of counts files) is required.\n")
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194 q(status = 1)
0
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195 }
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196
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197 if (is.null(opt$cpmReq)) {
14
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198 filt_cpm <- FALSE
0
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199 } else {
14
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200 filt_cpm <- TRUE
0
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201 }
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202
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203 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) {
14
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204 filt_smpcount <- FALSE
0
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205 } else {
14
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206 filt_smpcount <- TRUE
0
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207 }
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208
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209 if (is.null(opt$totReq)) {
14
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210 filt_totcount <- FALSE
0
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211 } else {
14
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212 filt_totcount <- TRUE
0
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213 }
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214
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215 if (is.null(opt$lrtOpt)) {
14
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216 want_lrt <- FALSE
0
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217 } else {
14
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218 want_lrt <- TRUE
0
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219 }
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220
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221 if (is.null(opt$rdaOpt)) {
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222 want_rda <- FALSE
0
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223 } else {
14
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224 want_rda <- TRUE
0
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225 }
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226
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227 if (is.null(opt$annoPath)) {
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228 have_anno <- FALSE
0
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229 } else {
14
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230 have_anno <- TRUE
0
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231 }
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232
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233 if (is.null(opt$normCounts)) {
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234 want_norm <- FALSE
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235 } else {
14
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236 want_norm <- TRUE
0
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237 }
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238
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239 if (is.null(opt$robOpt)) {
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240 want_robust <- FALSE
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241 } else {
14
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242 want_robust <- TRUE
0
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243 }
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244
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245
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246 if (!is.null(opt$filesPath)) {
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247 # Process the separate count files (adapted from DESeq2 wrapper)
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248 library("rjson")
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249 parser <- newJSONParser()
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250 parser$addData(opt$filesPath)
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251 factor_list <- parser$getObject()
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252 factors <- sapply(factor_list, function(x) x[[1]])
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253 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
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254 sampletable <- data.frame(
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255 sample = basename(filenames_in),
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256 filename = filenames_in,
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257 row.names = filenames_in,
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258 stringsAsFactors = FALSE
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259 )
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260 for (factor in factor_list) {
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261 factorname <- factor[[1]]
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262 sampletable[[factorname]] <- character(nrow(sampletable))
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263 lvls <- sapply(factor[[2]], function(x) names(x))
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264 for (i in seq_along(factor[[2]])) {
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265 files <- factor[[2]][[i]][[1]]
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266 sampletable[files, factorname] <- lvls[i]
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267 }
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268 sampletable[[factorname]] <- factor(sampletable[[factorname]], levels = lvls)
0
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269 }
14
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270 rownames(sampletable) <- sampletable$sample
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271 rem <- c("sample", "filename")
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272 factors <- sampletable[, !(names(sampletable) %in% rem), drop = FALSE]
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273
14
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274 # read in count files and create single table
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275 countfiles <- lapply(sampletable$filename, function(x) {
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276 read.delim(x, row.names = 1)
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277 })
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278 counts <- do.call("cbind", countfiles)
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279 } else {
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280 # Process the single count matrix
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281 counts <- read.table(opt$matrixPath, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = FALSE)
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282 row.names(counts) <- counts[, 1]
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283 counts <- counts[, -1]
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284 countsrows <- nrow(counts)
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285
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286 # Process factors
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287 if (is.null(opt$factInput)) {
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288 factordata <- read.table(opt$factFile, header = TRUE, sep = "\t", strip.white = TRUE, stringsAsFactors = TRUE)
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289 # check samples names match
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290 if (!any(factordata[, 1] %in% colnames(counts))) {
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291 stop("Sample IDs in factors file and count matrix don't match")
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292 }
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293 # order samples as in counts matrix
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294 factordata <- factordata[match(colnames(counts), factordata[, 1]), ]
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295 factors <- data.frame(sapply(factordata[, -1, drop = FALSE], make.names))
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296 } else {
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297 factors <- unlist(strsplit(opt$factInput, "|", fixed = TRUE))
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298 factordata <- list()
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299 for (fact in factors) {
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300 newfact <- unlist(strsplit(fact, split = "::"))
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301 factordata <- rbind(factordata, newfact)
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302 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
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303
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304 # Set the row names to be the name of the factor and delete first row
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305 row.names(factordata) <- factordata[, 1]
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306 factordata <- factordata[, -1]
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307 factordata <- sapply(factordata, sanitise_groups)
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308 factordata <- sapply(factordata, strsplit, split = ",")
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309 factordata <- sapply(factordata, make.names)
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310 # Transform factor data into data frame of R factor objects
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311 factors <- data.frame(factordata)
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312 }
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313 }
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314
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315 # if annotation file provided
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316 if (have_anno) {
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317 geneanno <- read.table(opt$annoPath, header = TRUE, sep = "\t", quote = "", strip.white = TRUE, stringsAsFactors = FALSE)
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318 }
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319
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320 # Create output directory
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321 out_path <- opt$outPath
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322 dir.create(out_path, showWarnings = FALSE)
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323
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324 # Check if contrastData is a file or not
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325 if (file.exists(opt$contrastData)) {
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326 contrast_data <- unlist(read.table(opt$contrastData, sep = "\t", header = TRUE)[[1]])
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327 } else {
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328 # Split up contrasts separated by comma into a vector then sanitise
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329 contrast_data <- unlist(strsplit(opt$contrastData, split = ","))
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330 }
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331 contrast_data <- sanitise_equation(contrast_data)
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332 contrast_data <- gsub(" ", ".", contrast_data, fixed = TRUE)
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333 # Convert colons to dots to match design matrix column name processing
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334 contrast_data <- gsub(":", ".", contrast_data, fixed = TRUE)
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335
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336 bcv_pdf <- make_out("bcvplot.pdf")
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337 bcv_png <- make_out("bcvplot.png")
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338 ql_pdf <- make_out("qlplot.pdf")
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339 ql_png <- make_out("qlplot.png")
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340 mds_pdf <- character() # Initialise character vector
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341 mds_png <- character()
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342 for (i in seq_len(ncol(factors))) {
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343 mds_pdf[i] <- make_out(paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".pdf"))
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344 mds_png[i] <- make_out(paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".png"))
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345 }
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346 md_pdf <- character()
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347 md_png <- character()
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348 top_out <- character()
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349 for (i in seq_along(contrast_data)) {
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350 md_pdf[i] <- make_out(paste0("mdplot_", sanitise_basename(contrast_data[i]), ".pdf"))
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351 md_png[i] <- make_out(paste0("mdplot_", sanitise_basename(contrast_data[i]), ".png"))
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352 top_out[i] <- make_out(paste0("edgeR_", sanitise_basename(contrast_data[i]), ".tsv"))
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353 } # Save output paths for each contrast as vectors
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354 norm_out <- make_out("edgeR_normcounts.tsv")
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355 rda_out <- make_out("edgeR_analysis.RData")
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356 session_out <- make_out("session_info.txt")
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357
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358 # Initialise data for html links and images, data frame with columns Label and
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359 # Link
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360 link_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
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361 image_data <- data.frame(Label = character(), Link = character(), stringsAsFactors = FALSE)
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362
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363 # Initialise vectors for storage of up/down/neutral regulated counts
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364 up_count <- numeric()
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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365 down_count <- numeric()
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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diff changeset
366 flat_count <- numeric()
0
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diff changeset
367
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
368 ################################################################################
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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369 ### Data Processing
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
370 ################################################################################
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
371
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
372 # Extract counts and annotation data
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
373 data <- list()
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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374 data$counts <- counts
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diff changeset
375 if (have_anno) {
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diff changeset
376 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
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diff changeset
377 annoord <- geneanno[match(row.names(counts), geneanno[, 1]), ]
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
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diff changeset
378 data$genes <- annoord
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
379 } else {
14
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diff changeset
380 data$genes <- data.frame(GeneID = row.names(counts))
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diff changeset
381 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
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382
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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383 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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384 # samples. Default is no filtering
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diff changeset
385 prefilter_count <- nrow(data$counts)
0
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386
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
387 if (filt_cpm || filt_smpcount || filt_totcount) {
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iuc
parents: 13
diff changeset
388 if (filt_totcount) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
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diff changeset
389 keep <- rowSums(data$counts) >= opt$cntReq
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
390 } else if (filt_smpcount) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
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diff changeset
391 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
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diff changeset
392 } else if (filt_cpm) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
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diff changeset
393 keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
394 }
0
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395
14
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diff changeset
396 data$counts <- data$counts[keep, ]
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
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diff changeset
397 data$genes <- data$genes[keep, , drop = FALSE]
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
398 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
399
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ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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diff changeset
400 postfilter_count <- nrow(data$counts)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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parents: 6
diff changeset
401 filtered_count <- prefilter_count - postfilter_count
0
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parents:
diff changeset
402
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
403 # Name rows of factors according to their sample
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
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diff changeset
404 row.names(factors) <- names(data$counts)
12
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
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diff changeset
405 factor_list <- names(factors)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
406
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
407 # Generating the DGEList object "data"
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
408 samplenames <- colnames(data$counts)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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parents: 6
diff changeset
409 genes <- data$genes
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
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diff changeset
410 data <- DGEList(data$counts)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
411 colnames(data) <- samplenames
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
412 data$samples <- factors
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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diff changeset
413 data$genes <- genes
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
414
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
415
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
416 if (!is.null(opt$formula)) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
417 formula <- opt$formula
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
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diff changeset
418 # sanitisation can be getting rid of the "~"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
419 if (!startsWith(formula, "~")) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
420 formula <- paste0("~", formula)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
421 }
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
422 } else {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
423 formula <- "~0"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
424 for (i in seq_along(factor_list)) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
425 formula <- paste(formula, factor_list[i], sep = "+")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
426 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
427 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
428
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
429 formula <- formula(formula)
12
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diff changeset
430 design <- model.matrix(formula, factors)
0
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431
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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diff changeset
432 for (i in seq_along(factor_list)) {
14
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diff changeset
433 colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
0
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diff changeset
434 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
435
15
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212
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diff changeset
436 # Ensure column names are syntactically valid
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212
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diff changeset
437 colnames(design) <- make.names(colnames(design))
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212
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diff changeset
438
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
439 # Calculating normalising factor, estimating dispersion
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ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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440 data <- calcNormFactors(data, method = opt$normOpt)
0
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diff changeset
441
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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diff changeset
442 if (want_robust) {
14
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diff changeset
443 data <- estimateDisp(data, design = design, robust = TRUE)
0
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parents:
diff changeset
444 } else {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
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diff changeset
445 data <- estimateDisp(data, design = design)
0
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iuc
parents:
diff changeset
446 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
447
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
448 # Generate contrasts information
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
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diff changeset
449 contrasts <- makeContrasts(contrasts = contrast_data, levels = design)
0
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parents:
diff changeset
450
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
451 ################################################################################
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
452 ### Data Output
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
453 ################################################################################
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
454
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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parents:
diff changeset
455 # Plot MDS
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
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diff changeset
456 labels <- names(counts)
3
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
457
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
458 # MDS plot
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
459 png(mds_png, width = 600, height = 600)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
460 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
461 img_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[1]), ".png")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
462 img_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[1]), ".png")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
463 image_data[1, ] <- c(img_name, img_addr)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
464 invisible(dev.off())
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
465
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
466 pdf(mds_pdf)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
467 plotMDS(data, labels = labels, col = as.numeric(factors[, 1]), cex = 0.8, main = paste("MDS Plot:", names(factors)[1]))
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
468 link_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[1]), ".pdf")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
469 link_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[1]), ".pdf")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
470 link_data[1, ] <- c(link_name, link_addr)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
471 invisible(dev.off())
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
472
3
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
473 # If additional factors create additional MDS plots coloured by factor
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
474 if (ncol(factors) > 1) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
475 for (i in 2:ncol(factors)) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
476 png(mds_png[i], width = 600, height = 600)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
477 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
478 img_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[i]), ".png")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
479 img_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".png")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
480 image_data <- rbind(image_data, c(img_name, img_addr))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
481 invisible(dev.off())
3
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
482
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
483 pdf(mds_pdf[i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
484 plotMDS(data, labels = labels, col = as.numeric(factors[, i]), cex = 0.8, main = paste("MDS Plot:", names(factors)[i]))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
485 link_name <- paste0("MDS Plot_", sanitise_basename(names(factors)[i]), ".pdf")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
486 link_addr <- paste0("mdsplot_", sanitise_basename(names(factors)[i]), ".pdf")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
487 link_data <- rbind(link_data, c(link_name, link_addr))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
488 invisible(dev.off())
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
489 }
3
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
490 }
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1
iuc
parents: 2
diff changeset
491
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
492 # BCV Plot
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
493 png(bcv_png, width = 600, height = 600)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
494 plotBCV(data, main = "BCV Plot")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
495 img_name <- "BCV Plot"
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
496 img_addr <- "bcvplot.png"
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
497 image_data <- rbind(image_data, c(img_name, img_addr))
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
498 invisible(dev.off())
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
499
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
500 pdf(bcv_pdf)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
501 plotBCV(data, main = "BCV Plot")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
502 link_name <- paste0("BCV Plot.pdf")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
503 link_addr <- paste0("bcvplot.pdf")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
504 link_data <- rbind(link_data, c(link_name, link_addr))
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
505 invisible(dev.off())
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
506
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
507 # Generate fit
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
508 if (want_lrt) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
509 fit <- glmFit(data, design)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
510 } else {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
511 if (want_robust) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
512 fit <- glmQLFit(data, design, robust = TRUE)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
513 } else {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
514 fit <- glmQLFit(data, design)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
515 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
516
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
517 # Plot QL dispersions
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
518 png(ql_png, width = 600, height = 600)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
519 plotQLDisp(fit, main = "QL Plot")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
520 img_name <- "QL Plot"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
521 img_addr <- "qlplot.png"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
522 image_data <- rbind(image_data, c(img_name, img_addr))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
523 invisible(dev.off())
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
524
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
525 pdf(ql_pdf)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
526 plotQLDisp(fit, main = "QL Plot")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
527 link_name <- "QL Plot.pdf"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
528 link_addr <- "qlplot.pdf"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
529 link_data <- rbind(link_data, c(link_name, link_addr))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
530 invisible(dev.off())
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
531 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
532
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
533 # Save normalised counts (log2cpm)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
534 if (want_norm) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
535 normalised_counts <- cpm(data, normalized.lib.sizes = TRUE, log = TRUE)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
536 normalised_counts <- data.frame(data$genes, normalised_counts)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
537 write.table(normalised_counts, file = norm_out, row.names = FALSE, sep = "\t", quote = FALSE)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
538 link_data <- rbind(link_data, c("edgeR_normcounts.tsv", "edgeR_normcounts.tsv"))
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
539 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
540
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
541
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
542 for (i in seq_along(contrast_data)) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
543 if (want_lrt) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
544 res <- glmLRT(fit, contrast = contrasts[, i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
545 } else {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
546 res <- glmQLFTest(fit, contrast = contrasts[, i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
547 }
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
548
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
549 status <- decideTestsDGE(res,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
550 adjust.method = opt$pAdjOpt, p.value = opt$pValReq,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
551 lfc = opt$lfcReq
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
552 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
553 sum_status <- summary(status)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
554
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
555 # Collect counts for differential expression
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
556 up_count[i] <- sum_status["Up", ]
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
557 down_count[i] <- sum_status["Down", ]
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
558 flat_count[i] <- sum_status["NotSig", ]
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
559
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
560 # Write top expressions table
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
561 top <- topTags(res, adjust.method = opt$pAdjOpt, n = Inf, sort.by = "PValue")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
562 write.table(top, file = top_out[i], row.names = FALSE, sep = "\t", quote = FALSE)
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
563
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
564 link_name <- paste0("edgeR_", sanitise_basename(contrast_data[i]), ".tsv")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
565 link_addr <- paste0("edgeR_", sanitise_basename(contrast_data[i]), ".tsv")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
566 link_data <- rbind(link_data, c(link_name, link_addr))
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
567
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
568 # Plot MD (log ratios vs mean difference) using limma package
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
569 pdf(md_pdf[i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
570 limma::plotMD(res,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
571 status = status,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
572 main = paste("MD Plot:", unmake_names(contrast_data[i])),
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
573 hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
574 xlab = "Average Expression", ylab = "logFC"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
575 )
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
576
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
577 abline(h = 0, col = "grey", lty = 2)
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
578
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
579 link_name <- paste0("MD Plot_", sanitise_basename(contrast_data[i]), ".pdf")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
580 link_addr <- paste0("mdplot_", sanitise_basename(contrast_data[i]), ".pdf")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
581 link_data <- rbind(link_data, c(link_name, link_addr))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
582 invisible(dev.off())
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
583
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
584 png(md_png[i], height = 600, width = 600)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
585 limma::plotMD(res,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
586 status = status,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
587 main = paste("MD Plot:", unmake_names(contrast_data[i])),
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
588 hl.col = alpha(c("firebrick", "blue"), 0.4), values = c(1, -1),
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
589 xlab = "Average Expression", ylab = "logFC"
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
590 )
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
591
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
592 abline(h = 0, col = "grey", lty = 2)
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
593
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
594 img_name <- paste0("MD Plot_", sanitise_basename(contrast_data[i]), ".png")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
595 img_addr <- paste0("mdplot_", sanitise_basename(contrast_data[i]), ".png")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
596 image_data <- rbind(image_data, c(img_name, img_addr))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
597 invisible(dev.off())
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
598 }
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
599 sig_diff <- data.frame(Up = up_count, Flat = flat_count, Down = down_count)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
600 row.names(sig_diff) <- contrast_data
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
601
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
602 # Save relevant items as rda object
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
603 if (want_rda) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
604 if (want_norm) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
605 save(counts, data, status, normalised_counts, labels, factors, fit, res, top, contrasts, design,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
606 file = rda_out, ascii = TRUE
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
607 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
608 } else {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
609 save(counts, data, status, labels, factors, fit, res, top, contrasts, design,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
610 file = rda_out, ascii = TRUE
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
611 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
612 }
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
613 link_data <- rbind(link_data, c("edgeR_analysis.RData", "edgeR_analysis.RData"))
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
614 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
615
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
616 # Record session info
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
617 writeLines(capture.output(sessionInfo()), session_out)
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
618 link_data <- rbind(link_data, c("Session Info", "session_info.txt"))
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
619
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
620 # Record ending time and calculate total run time
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
621 time_end <- as.character(Sys.time())
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
622 time_taken <- capture.output(round(difftime(time_end, time_start), digits = 3))
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
623 time_taken <- gsub("Time difference of ", "", time_taken, fixed = TRUE)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
624
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
625 ################################################################################
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
626 ### HTML Generation
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
627 ################################################################################
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
628
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
629 # Clear file
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
630 cat("", file = opt$htmlPath)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
631
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
632 cata("<html>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
633
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
634 cata("<body>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
635 cata("<h3>edgeR Analysis Output:</h3>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
636 cata("Links to PDF copies of plots are in 'Plots' section below.<br />\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
637
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
638 html_image(image_data$Link[1], image_data$Label[1])
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
639
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
640 for (i in 2:nrow(image_data)) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
641 html_image(image_data$Link[i], image_data$Label[i])
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
642 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
643
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
644 cata("<h4>Differential Expression Counts:</h4>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
645
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
646 cata("<table border=\"1\" cellpadding=\"4\">\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
647 cata("<tr>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
648 table_item()
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
649 for (i in colnames(sig_diff)) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
650 table_head_item(i)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
651 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
652 cata("</tr>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
653 for (i in seq_len(nrow(sig_diff))) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
654 cata("<tr>\n")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
655 table_head_item(unmake_names(row.names(sig_diff)[i]))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
656 for (j in seq_len(ncol(sig_diff))) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
657 table_item(as.character(sig_diff[i, j]))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
658 }
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
659 cata("</tr>\n")
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
660 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
661 cata("</table>")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
662
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
663 cata("<h4>Plots:</h4>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
664 for (i in seq_len(nrow(link_data))) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
665 if (grepl(".pdf", link_data$Link[i])) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
666 html_link(link_data$Link[i], link_data$Label[i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
667 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
668 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
669
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
670 cata("<h4>Tables:</h4>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
671 for (i in seq_len(nrow(link_data))) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
672 if (grepl(".tsv", link_data$Link[i])) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
673 html_link(link_data$Link[i], link_data$Label[i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
674 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
675 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
676
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
677 if (want_rda) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
678 cata("<h4>R Data Objects:</h4>\n")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
679 for (i in seq_len(nrow(link_data))) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
680 if (grepl(".RData", link_data$Link[i])) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
681 html_link(link_data$Link[i], link_data$Label[i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
682 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
683 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
684 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
685
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
686 cata("<p>Alt-click links to download file.</p>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
687 cata("<p>Click floppy disc icon associated history item to download ")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
688 cata("all files.</p>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
689 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
690
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
691 cata("<h4>Additional Information</h4>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
692 cata("<ul>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
693
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
694 if (filt_cpm || filt_smpcount || filt_totcount) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
695 if (filt_cpm) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
696 temp_str <- paste(
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
697 "Genes without more than", opt$cpmReq,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
698 "CPM in at least", opt$sampleReq, "samples are insignificant",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
699 "and filtered out."
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
700 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
701 } else if (filt_smpcount) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
702 temp_str <- paste(
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
703 "Genes without more than", opt$cntReq,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
704 "counts in at least", opt$sampleReq, "samples are insignificant",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
705 "and filtered out."
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
706 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
707 } else if (filt_totcount) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
708 temp_str <- paste(
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
709 "Genes without more than", opt$cntReq,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
710 "counts, after summing counts for all samples, are insignificant",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
711 "and filtered out."
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
712 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
713 }
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
714
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
715 list_item(temp_str)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
716 filter_prop <- round(filtered_count / prefilter_count * 100, digits = 2)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
717 temp_str <- paste0(
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
718 filtered_count, " of ", prefilter_count, " (", filter_prop,
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
719 "%) genes were filtered out for low expression."
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
720 )
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
721 list_item(temp_str)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
722 }
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
723 list_item(opt$normOpt, " was the method used to normalise library sizes.")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
724 if (want_lrt) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
725 list_item("The edgeR likelihood ratio test was used.")
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
726 } else {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
727 if (want_robust) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
728 list_item("The edgeR quasi-likelihood test was used with robust settings (robust=TRUE with estimateDisp and glmQLFit).")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
729 } else {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
730 list_item("The edgeR quasi-likelihood test was used.")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
731 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
732 }
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
733 if (opt$pAdjOpt != "none") {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
734 if (opt$pAdjOpt == "BH" || opt$pAdjOpt == "BY") {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
735 temp_str <- paste0(
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
736 "MD-Plot highlighted genes are significant at FDR ",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
737 "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
738 "least ", opt$lfcReq, "."
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
739 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
740 list_item(temp_str)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
741 } else if (opt$pAdjOpt == "holm") {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
742 temp_str <- paste0(
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
743 "MD-Plot highlighted genes are significant at adjusted ",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
744 "p-value of ", opt$pValReq, " by the Holm(1979) ",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
745 "method, and exhibit log2-fold-change of at least ",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
746 opt$lfcReq, "."
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
747 )
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
748 list_item(temp_str)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
749 }
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
750 } else {
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
751 temp_str <- paste0(
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
752 "MD-Plot highlighted genes are significant at p-value ",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
753 "of ", opt$pValReq, " and exhibit log2-fold-change of at ",
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
754 "least ", opt$lfcReq, "."
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
755 )
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
756 list_item(temp_str)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
757 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
758 cata("</ul>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
759
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
760 cata("<h4>Summary of experimental data:</h4>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
761
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
762 cata("<p>*CHECK THAT SAMPLES ARE ASSOCIATED WITH CORRECT GROUP(S)*</p>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
763
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
764 cata("<table border=\"1\" cellpadding=\"3\">\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
765 cata("<tr>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
766 table_head_item("SampleID")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
767 table_head_item(names(factors)[1], " (Primary Factor)")
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
768
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
769 if (ncol(factors) > 1) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
770 for (i in names(factors)[2:length(names(factors))]) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
771 table_head_item(i)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
772 }
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
773 cata("</tr>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
774 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
775
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
776 for (i in seq_len(nrow((factors)))) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
777 cata("<tr>\n")
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
778 table_head_item(row.names(factors)[i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
779 for (j in seq_len(ncol(factors))) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
780 table_item(as.character(unmake_names(factors[i, j])))
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
781 }
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
782 cata("</tr>\n")
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
783 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
784 cata("</table>")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
785
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
786 for (i in seq_len(nrow(link_data))) {
14
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
787 if (grepl("session_info", link_data$Link[i])) {
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
788 html_link(link_data$Link[i], link_data$Label[i])
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670
iuc
parents: 13
diff changeset
789 }
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
790 }
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
791
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
792 cata("<table border=\"0\">\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
793 cata("<tr>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
794 table_item("Task started at:")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
795 table_item(time_start)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
796 cata("</tr>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
797 cata("<tr>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
798 table_item("Task ended at:")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
799 table_item(time_end)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
800 cata("</tr>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
801 cata("<tr>\n")
8
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
802 table_item("Task run time:")
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc"
iuc
parents: 6
diff changeset
803 table_item(time_taken)
0
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
804 cata("<tr>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
805 cata("</table>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
806
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
807 cata("</body>\n")
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d
iuc
parents:
diff changeset
808 cata("</html>")