Mercurial > repos > iuc > limma_voom

annotate limma_voom.R @ 6:39fa12a6d885 draft

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author iuc
date Tue, 08 May 2018 18:12:40 -0400
parents d8a55b5f0de0
children e6a4ff41af6b
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1 # This tool takes in a matrix of feature counts as well as gene annotations and
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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 # annoPath", "a", 2, "character" -Path to input containing gene annotations
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12 # contrastData", "C", 1, "character" -String containing contrasts of interest
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13 # cpmReq", "c", 2, "double" -Float specifying cpm requirement
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14 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement
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15 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement
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16 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output
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17 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output
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18 # lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement
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19 # pValReq", "p", 1, "double" -Float specifying the p-value requirement
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20 # pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method
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21 # normOpt", "n", 1, "character" -String specifying type of normalisation used
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22 # robOpt", "b", 0, "logical" -String specifying if robust options should be used
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23 # trend", "t", 1, "double" -Float for prior.count if limma-trend is used instead of voom
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24 # weightOpt", "w", 0, "logical" -String specifying if voomWithQualityWeights should be used
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25 # volhiOpt", "v", 1, "integer" -Integer specifying number of genes to highlight in volcano plot
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26 # treatOpt", "T", 0, "logical" -String specifying if TREAT function shuld be used
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27 #
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28 # OUT:
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29 # MDS Plot
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30 # Voom/SA plot
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31 # MD Plot
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32 # Expression Table
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33 # HTML file linking to the ouputs
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34 # Optional:
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35 # Normalised counts Table
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36 # RData file
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37 #
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38 #
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39 # Author: Shian Su - registertonysu@gmail.com - Jan 2014
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40 # Modified by: Maria Doyle - Jun 2017, Jan 2018
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42 # Record starting time
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43 timeStart <- as.character(Sys.time())
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45 # Load all required libraries
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46 library(methods, quietly=TRUE, warn.conflicts=FALSE)
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47 library(statmod, quietly=TRUE, warn.conflicts=FALSE)
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48 library(splines, quietly=TRUE, warn.conflicts=FALSE)
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49 library(edgeR, quietly=TRUE, warn.conflicts=FALSE)
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50 library(limma, quietly=TRUE, warn.conflicts=FALSE)
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51 library(scales, quietly=TRUE, warn.conflicts=FALSE)
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52 library(getopt, quietly=TRUE, warn.conflicts=FALSE)
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54 ################################################################################
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55 ### Function Declaration
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56 ################################################################################
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57 # Function to sanitise contrast equations so there are no whitespaces
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58 # surrounding the arithmetic operators, leading or trailing whitespace
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59 sanitiseEquation <- function(equation) {
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60 equation <- gsub(" *[+] *", "+", equation)
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61 equation <- gsub(" *[-] *", "-", equation)
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62 equation <- gsub(" *[/] *", "/", equation)
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63 equation <- gsub(" *[*] *", "*", equation)
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64 equation <- gsub("^\\s+|\\s+$", "", equation)
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65 return(equation)
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66 }
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68 # Function to sanitise group information
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69 sanitiseGroups <- function(string) {
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70 string <- gsub(" *[,] *", ",", string)
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71 string <- gsub("^\\s+|\\s+$", "", string)
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72 return(string)
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73 }
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75 # Function to change periods to whitespace in a string
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76 unmake.names <- function(string) {
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77 string <- gsub(".", " ", string, fixed=TRUE)
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78 return(string)
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79 }
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81 # Generate output folder and paths
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82 makeOut <- function(filename) {
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83 return(paste0(opt$outPath, "/", filename))
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84 }
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85
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86 # Generating design information
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87 pasteListName <- function(string) {
3
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88 return(paste0("factors$", string))
0
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89 }
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90
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91 # Create cata function: default path set, default seperator empty and appending
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92 # true by default (Ripped straight from the cat function with altered argument
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93 # defaults)
3
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94 cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL,
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95 append = TRUE) {
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96 if (is.character(file))
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97 if (file == "")
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98 file <- stdout()
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99 else if (substring(file, 1L, 1L) == "|") {
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100 file <- pipe(substring(file, 2L), "w")
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101 on.exit(close(file))
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102 }
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103 else {
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104 file <- file(file, ifelse(append, "a", "w"))
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105 on.exit(close(file))
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106 }
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107 .Internal(cat(list(...), file, sep, fill, labels, append))
0
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108 }
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109
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110 # Function to write code for html head and title
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111 HtmlHead <- function(title) {
3
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112 cata("<head>\n")
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113 cata("<title>", title, "</title>\n")
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114 cata("</head>\n")
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115 }
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116
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117 # Function to write code for html links
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118 HtmlLink <- function(address, label=address) {
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119 cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n")
0
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120 }
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121
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122 # Function to write code for html images
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123 HtmlImage <- function(source, label=source, height=600, width=600) {
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124 cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height)
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125 cata("\" width=\"", width, "\"/>\n")
0
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126 }
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127
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128 # Function to write code for html list items
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129 ListItem <- function(...) {
3
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130 cata("<li>", ..., "</li>\n")
0
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131 }
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132
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133 TableItem <- function(...) {
3
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134 cata("<td>", ..., "</td>\n")
0
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135 }
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136
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137 TableHeadItem <- function(...) {
3
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138 cata("<th>", ..., "</th>\n")
0
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139 }
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140
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141 ################################################################################
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142 ### Input Processing
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143 ################################################################################
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144
3
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145 # Collect arguments from command line
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146 args <- commandArgs(trailingOnly=TRUE)
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147
3
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148 # Get options, using the spec as defined by the enclosed list.
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149 # Read the options from the default: commandArgs(TRUE).
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150 spec <- matrix(c(
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151 "htmlPath", "R", 1, "character",
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152 "outPath", "o", 1, "character",
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153 "filesPath", "j", 2, "character",
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154 "matrixPath", "m", 2, "character",
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155 "factFile", "f", 2, "character",
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156 "factInput", "i", 2, "character",
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157 "annoPath", "a", 2, "character",
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158 "contrastData", "C", 1, "character",
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159 "cpmReq", "c", 1, "double",
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160 "totReq", "y", 0, "logical",
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161 "cntReq", "z", 1, "integer",
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162 "sampleReq", "s", 1, "integer",
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163 "normCounts", "x", 0, "logical",
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164 "rdaOpt", "r", 0, "logical",
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165 "lfcReq", "l", 1, "double",
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166 "pValReq", "p", 1, "double",
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167 "pAdjOpt", "d", 1, "character",
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168 "normOpt", "n", 1, "character",
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169 "robOpt", "b", 0, "logical",
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170 "trend", "t", 1, "double",
6
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171 "weightOpt", "w", 0, "logical",
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172 "volhiOpt", "v", 1, "integer",
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173 "treatOpt", "T", 0, "logical"),
3
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174 byrow=TRUE, ncol=4)
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175 opt <- getopt(spec)
0
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176
1
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177
3
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178 if (is.null(opt$matrixPath) & is.null(opt$filesPath)) {
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179 cat("A counts matrix (or a set of counts files) is required.\n")
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180 q(status=1)
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181 }
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182
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183 if (is.null(opt$cpmReq)) {
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184 filtCPM <- FALSE
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185 } else {
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186 filtCPM <- TRUE
1
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187 }
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188
3
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189 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) {
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190 filtSmpCount <- FALSE
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191 } else {
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192 filtSmpCount <- TRUE
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193 }
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194
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195 if (is.null(opt$totReq)) {
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196 filtTotCount <- FALSE
0
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197 } else {
3
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198 filtTotCount <- TRUE
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199 }
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200
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201 if (is.null(opt$rdaOpt)) {
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202 wantRda <- FALSE
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203 } else {
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204 wantRda <- TRUE
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205 }
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206
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207 if (is.null(opt$annoPath)) {
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208 haveAnno <- FALSE
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209 } else {
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210 haveAnno <- TRUE
0
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211 }
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212
3
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213 if (is.null(opt$normCounts)) {
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214 wantNorm <- FALSE
0
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215 } else {
3
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216 wantNorm <- TRUE
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217 }
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218
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219 if (is.null(opt$robOpt)) {
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220 wantRobust <- FALSE
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221 } else {
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222 wantRobust <- TRUE
0
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223 }
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224
3
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225 if (is.null(opt$weightOpt)) {
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226 wantWeight <- FALSE
0
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227 } else {
3
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228 wantWeight <- TRUE
0
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229 }
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230
3
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231 if (is.null(opt$trend)) {
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232 wantTrend <- FALSE
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233 deMethod <- "limma-voom"
1
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234 } else {
3
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235 wantTrend <- TRUE
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236 deMethod <- "limma-trend"
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237 priorCount <- opt$trend
1
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238 }
0
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239
6
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240 if (is.null(opt$treatOpt)) {
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241 wantTreat <- FALSE
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242 } else {
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243 wantTreat <- TRUE
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244 }
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245
0
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246
3
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247 if (!is.null(opt$filesPath)) {
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248 # Process the separate count files (adapted from DESeq2 wrapper)
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249 library("rjson")
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250 parser <- newJSONParser()
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251 parser$addData(opt$filesPath)
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252 factorList <- parser$getObject()
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253 factors <- sapply(factorList, function(x) x[[1]])
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254 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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255 sampleTable <- data.frame(sample=basename(filenamesIn),
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256 filename=filenamesIn,
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257 row.names=filenamesIn,
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diff changeset
258 stringsAsFactors=FALSE)
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diff changeset
259 for (factor in factorList) {
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260 factorName <- factor[[1]]
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261 sampleTable[[factorName]] <- character(nrow(sampleTable))
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262 lvls <- sapply(factor[[2]], function(x) names(x))
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diff changeset
263 for (i in seq_along(factor[[2]])) {
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264 files <- factor[[2]][[i]][[1]]
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265 sampleTable[files,factorName] <- lvls[i]
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266 }
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267 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls)
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268 }
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269 rownames(sampleTable) <- sampleTable$sample
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270 rem <- c("sample","filename")
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271 factors <- sampleTable[, !(names(sampleTable) %in% rem), drop=FALSE]
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272
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273 #read in count files and create single table
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274 countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)})
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275 counts <- do.call("cbind", countfiles)
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276
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277 } else {
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278 # Process the single count matrix
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279 counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", stringsAsFactors=FALSE)
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280 row.names(counts) <- counts[, 1]
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281 counts <- counts[ , -1]
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282 countsRows <- nrow(counts)
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283
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284 # Process factors
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285 if (is.null(opt$factInput)) {
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286 factorData <- read.table(opt$factFile, header=TRUE, sep="\t")
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287 factors <- factorData[, -1, drop=FALSE]
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288 } else {
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289 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE))
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290 factorData <- list()
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291 for (fact in factors) {
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292 newFact <- unlist(strsplit(fact, split="::"))
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293 factorData <- rbind(factorData, newFact)
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294 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor.
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295
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296 # Set the row names to be the name of the factor and delete first row
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297 row.names(factorData) <- factorData[, 1]
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298 factorData <- factorData[, -1]
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299 factorData <- sapply(factorData, sanitiseGroups)
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300 factorData <- sapply(factorData, strsplit, split=",")
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301 factorData <- sapply(factorData, make.names)
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302 # Transform factor data into data frame of R factor objects
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303 factors <- data.frame(factorData)
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304 }
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305 }
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306
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307 # if annotation file provided
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308 if (haveAnno) {
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309 geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", stringsAsFactors=FALSE)
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310 }
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311
0
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312 #Create output directory
3
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313 dir.create(opt$outPath, showWarnings=FALSE)
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314
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315 # Split up contrasts seperated by comma into a vector then sanitise
3
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316 contrastData <- unlist(strsplit(opt$contrastData, split=","))
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317 contrastData <- sanitiseEquation(contrastData)
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318 contrastData <- gsub(" ", ".", contrastData, fixed=TRUE)
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319
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320 denOutPng <- makeOut("densityplots.png")
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321 denOutPdf <- makeOut("DensityPlots.pdf")
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322 boxOutPng <- makeOut("boxplots.png")
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323 boxOutPdf <- makeOut("BoxPlots.pdf")
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324 mdsOutPdf <- character() # Initialise character vector
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325 mdsOutPng <- character()
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326 for (i in 1:ncol(factors)) {
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327 mdsOutPdf[i] <- makeOut(paste0("mdsplot_", names(factors)[i], ".pdf"))
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328 mdsOutPng[i] <- makeOut(paste0("mdsplot_", names(factors)[i], ".png"))
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329 }
3
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330
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331 mdOutPdf <- character()
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332 volOutPdf <- character()
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333 mdvolOutPng <- character()
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334 topOut <- character()
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335 for (i in 1:length(contrastData)) {
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336 mdOutPdf[i] <- makeOut(paste0("mdplot_", contrastData[i], ".pdf"))
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337 volOutPdf[i] <- makeOut(paste0("volplot_", contrastData[i], ".pdf"))
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338 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", contrastData[i], ".png"))
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339 topOut[i] <- makeOut(paste0(deMethod, "_", contrastData[i], ".tsv"))
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340 }
6
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341
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342 normOut <- makeOut(paste0(deMethod, "_normcounts.tsv"))
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343 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData"))
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344 sessionOut <- makeOut("session_info.txt")
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345
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346 # Initialise data for html links and images, data frame with columns Label and
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347 # Link
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348 linkData <- data.frame(Label=character(), Link=character(),
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349 stringsAsFactors=FALSE)
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350 imageData <- data.frame(Label=character(), Link=character(),
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351 stringsAsFactors=FALSE)
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352
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353 # Initialise vectors for storage of up/down/neutral regulated counts
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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354 upCount <- numeric()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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355 downCount <- numeric()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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356 flatCount <- numeric()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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357
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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358 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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359 ### Data Processing
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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360 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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361
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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362 # Extract counts and annotation data
3
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363 print("Extracting counts")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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364 data <- list()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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365 data$counts <- counts
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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366 if (haveAnno) {
4
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367 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno)
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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368 annoord <- geneanno[match(row.names(counts), geneanno[,1]), ]
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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369 data$genes <- annoord
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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370 } else {
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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371 data$genes <- data.frame(GeneID=row.names(counts))
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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372 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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373
3
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374 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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375 # samples. Default is no filtering
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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376 preFilterCount <- nrow(data$counts)
3
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377
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378 if (filtCPM || filtSmpCount || filtTotCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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379
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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380 if (filtTotCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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381 keep <- rowSums(data$counts) >= opt$cntReq
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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382 } else if (filtSmpCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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383 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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384 } else if (filtCPM) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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385 keep <- rowSums(cpm(data$counts) >= opt$cpmReq) >= opt$sampleReq
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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386 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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387
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388 data$counts <- data$counts[keep, ]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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389 data$genes <- data$genes[keep, , drop=FALSE]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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390 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
391
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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392 postFilterCount <- nrow(data$counts)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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393 filteredCount <- preFilterCount-postFilterCount
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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394
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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395 # Creating naming data
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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396 samplenames <- colnames(data$counts)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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397 sampleanno <- data.frame("sampleID"=samplenames, factors)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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398
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
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399
6
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400 # Generating the DGEList object "y"
3
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401 print("Generating DGEList object")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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402 data$samples <- sampleanno
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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403 data$samples$lib.size <- colSums(data$counts)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
404 data$samples$norm.factors <- 1
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
405 row.names(data$samples) <- colnames(data$counts)
6
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406 y <- new("DGEList", data)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
407
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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408 print("Generating Design")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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409 # Name rows of factors according to their sample
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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410 row.names(factors) <- names(data$counts)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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411 factorList <- sapply(names(factors), pasteListName)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
412 formula <- "~0"
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff changeset
413 for (i in 1:length(factorList)) {
1
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414 formula <- paste(formula,factorList[i], sep="+")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
415 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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416 formula <- formula(formula)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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417 design <- model.matrix(formula)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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418 for (i in 1:length(factorList)) {
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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419 colnames(design) <- gsub(factorList[i], "", colnames(design), fixed=TRUE)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
420 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
421
3
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parents: 2
diff changeset
422 # Calculating normalising factors
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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423 print("Calculating Normalisation Factors")
6
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424 y <- calcNormFactors(y, method=opt$normOpt)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
diff changeset
425
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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426 # Generate contrasts information
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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427 print("Generating Contrasts")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
428 contrasts <- makeContrasts(contrasts=contrastData, levels=design)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
429
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
430 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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diff changeset
431 ### Data Output
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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432 ################################################################################
6
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diff changeset
433
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
434 # Plot Density (if filtering low counts)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
435 if (filtCPM || filtSmpCount || filtTotCount) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
436 nsamples <- ncol(counts)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
437
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
438 # PNG
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iuc
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439 png(denOutPng, width=1200, height=600)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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440 par(mfrow=c(1,2), cex.axis=0.8)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
441
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
442 # before filtering
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
443 logcpm <- cpm(counts, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
444 plot(density(logcpm[,1]), col=as.numeric(factors[1, 1]), lwd=2, las=2, main="", xlab="")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
445 title(main="Density Plot: Raw counts", xlab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
446 for (i in 2:nsamples){
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
447 den <- density(logcpm[,i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
448 lines(den$x, den$y, col=as.numeric(factors[i, 1]), lwd=2)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
449 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
450
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
451 # after filtering
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
452 logcpm <- cpm(data$counts, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
453 plot(density(logcpm[,1]), col=as.numeric(factors[1, 1]), lwd=2, las=2, main="", xlab="")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
454 title(main="Density Plot: Filtered counts", xlab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
455 for (i in 2:nsamples){
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
456 den <- density(logcpm[,i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
457 lines(den$x, den$y, col=as.numeric(factors[i, 1]), lwd=2)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
458 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
459 legend("topright", samplenames, text.col=as.numeric(factors[, 1]), bty="n")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
460 imgName <- "Densityplots.png"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
461 imgAddr <- "densityplots.png"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
462 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
463 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
464
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
465 # PDF
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
466 pdf(denOutPdf, width=14)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
467 par(mfrow=c(1,2), cex.axis=0.8)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
468 logcpm <- cpm(counts, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
469 plot(density(logcpm[,1]), col=as.numeric(factors[1, 1]), lwd=2, las=2, main="", xlab="")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
470 title(main="Density Plot: Raw counts", xlab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
471 for (i in 2:nsamples){
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
472 den <- density(logcpm[,i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
473 lines(den$x, den$y, col=as.numeric(factors[i, 1]), lwd=2)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
474 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
475 logcpm <- cpm(data$counts, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
476 plot(density(logcpm[,1]), col=as.numeric(factors[1, 1]), lwd=2, las=2, main="", xlab="")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
477 title(main="Density Plot: Filtered counts", xlab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
478 for (i in 2:nsamples){
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
479 den <- density(logcpm[,i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
480 lines(den$x, den$y, col=as.numeric(factors[i, 1]), lwd=2)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
481 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
482 legend("topright", samplenames, text.col=as.numeric(factors[, 1]), bty="n")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
483 linkName <- "DensityPlots.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
484 linkAddr <- "densityplots.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
485 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
486 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
487 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
488
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
489 # Plot Box plots (before and after normalisation)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
490 if (opt$normOpt != "none") {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
491 png(boxOutPng, width=1200, height=600)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
492 par(mfrow=c(1,2), cex.axis=0.8)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
493 logcpm <- cpm(y$counts, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
494 boxplot(logcpm, las=2, col=as.numeric(factors[, 1]))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
495 abline(h=median(logcpm), col=4)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
496 title(main="Box Plot: Unnormalised counts", ylab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
497 lcpm <- cpm(y, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
498 boxplot(lcpm, las=2, col=as.numeric(factors[, 1]))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
499 abline(h=median(lcpm), col=4)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
500 title(main="Box Plot: Normalised counts", ylab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
501 imgName <- "Boxplots.png"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
502 imgAddr <- "boxplots.png"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
503 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
504 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
505
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
506 pdf(boxOutPdf, width=14)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
507 par(mfrow=c(1,2), cex.axis=0.8)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
508 logcpm <- cpm(y$counts, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
509 boxplot(logcpm, las=2, col=as.numeric(factors[, 1]))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
510 abline(h=median(logcpm), col=4)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
511 title(main="Box Plot: Unnormalised counts", ylab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
512 lcpm <- cpm(y, log=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
513 boxplot(lcpm, las=2, col=as.numeric(factors[, 1]))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
514 abline(h=median(lcpm), col=4)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
515 title(main="Box Plot: Normalised counts", ylab="Log-cpm")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
516 linkName <- "BoxPlots.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
517 linkAddr <- "boxplots.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
518 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
519 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
520 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
521
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
diff changeset
522 # Plot MDS
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
523 print("Generating MDS plot")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
diff changeset
524 labels <- names(counts)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
525
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
526 for (i in 1:ncol(factors)) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
527 png(mdsOutPng[i], width=600, height=600)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
528 plotMDS(y, labels=labels, col=as.numeric(factors[, i]), cex=0.8, main=paste("MDS Plot:", names(factors)[i]))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
529 imgName <- paste0("MDSPlot_", names(factors)[i], ".png")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
530 imgAddr <- paste0("mdsplot_", names(factors)[i], ".png")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
531 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
532 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
533
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
534 pdf(mdsOutPdf[i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
535 plotMDS(y, labels=labels, col=as.numeric(factors[, i]), cex=0.8, main=paste("MDS Plot:", names(factors)[i]))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
536 linkName <- paste0("MDSPlot_", names(factors)[i], ".pdf")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
537 linkAddr <- paste0("mdsplot_", names(factors)[i], ".pdf")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
538 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
539 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
540 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
541
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
542 if (wantTrend) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
543 # limma-trend approach
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
544 logCPM <- cpm(y, log=TRUE, prior.count=opt$trend)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
545 fit <- lmFit(logCPM, design)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
546 fit$genes <- y$genes
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
547 fit <- contrasts.fit(fit, contrasts)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
548 if (wantRobust) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
549 fit <- eBayes(fit, trend=TRUE, robust=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
550 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
551 fit <- eBayes(fit, trend=TRUE, robust=FALSE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
552 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
553 # plot fit with plotSA
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
554 saOutPng <- makeOut("saplot.png")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
555 saOutPdf <- makeOut("saplot.pdf")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
556
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
557 png(saOutPng, width=600, height=600)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
558 plotSA(fit, main="SA Plot")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
559 imgName <- "SAPlot.png"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
560 imgAddr <- "saplot.png"
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
561 imageData <- rbind(imageData, c(imgName, imgAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
562 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
563
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
564 pdf(saOutPdf, width=14)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
565 plotSA(fit, main="SA Plot")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
566 linkName <- "SAPlot.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
567 linkAddr <- "saplot.pdf"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
568 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
569 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
570
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
571 plotData <- logCPM
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
572
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
573 # Save normalised counts (log2cpm)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
574 if (wantNorm) {
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
575 write.table(logCPM, file=normOut, row.names=TRUE, sep="\t", quote=FALSE)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
576 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv"))))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
577 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
578 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
579 # limma-voom approach
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
580 voomOutPdf <- makeOut("voomplot.pdf")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
581 voomOutPng <- makeOut("voomplot.png")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
582
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
583 if (wantWeight) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
584 # Creating voom data object and plot
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
585 png(voomOutPng, width=1000, height=600)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
586 vData <- voomWithQualityWeights(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
587 imgName <- "VoomPlot.png"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
588 imgAddr <- "voomplot.png"
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
589 imageData <- rbind(imageData, c(imgName, imgAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
590 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
591
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
592 pdf(voomOutPdf, width=14)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
593 vData <- voomWithQualityWeights(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
594 linkName <- "VoomPlot.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
595 linkAddr <- "voomplot.pdf"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
596 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
597 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
598
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
599 # Generating fit data and top table with weights
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
600 wts <- vData$weights
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
601 voomFit <- lmFit(vData, design, weights=wts)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
602
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
603 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
604 # Creating voom data object and plot
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
605 png(voomOutPng, width=600, height=600)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
606 vData <- voom(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
607 imgName <- "VoomPlot"
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
608 imgAddr <- "voomplot.png"
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
609 imageData <- rbind(imageData, c(imgName, imgAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
610 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
611
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
612 pdf(voomOutPdf)
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
613 vData <- voom(y, design=design, plot=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
614 linkName <- "VoomPlot.pdf"
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
615 linkAddr <- "voomplot.pdf"
3
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616 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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617 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
618
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
619 # Generate voom fit
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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620 voomFit <- lmFit(vData, design)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
621 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
622
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
623 # Save normalised counts (log2cpm)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
624 if (wantNorm) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
625 norm_counts <- data.frame(vData$genes, vData$E)
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
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parents: 3
diff changeset
626 write.table(norm_counts, file=normOut, row.names=FALSE, sep="\t", quote=FALSE)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
627 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts.tsv"))))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
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628 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
629
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
630 # Fit linear model and estimate dispersion with eBayes
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
631 voomFit <- contrasts.fit(voomFit, contrasts)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
632 if (wantRobust) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
633 fit <- eBayes(voomFit, robust=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
diff changeset
634 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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635 fit <- eBayes(voomFit, robust=FALSE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
636 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
637 plotData <- vData
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
638 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
639
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
diff changeset
640
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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diff changeset
641 print("Generating DE results")
6
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parents: 5
diff changeset
642
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
643 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
644 print("Applying TREAT method")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
645 if (wantRobust) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
646 fit <- treat(fit, lfc=opt$lfcReq, robust=TRUE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
647 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
648 fit <- treat(fit, lfc=opt$lfcReq, robust=FALSE)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
649 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
650 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
651
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
652 status = decideTests(fit, adjust.method=opt$pAdjOpt, p.value=opt$pValReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
653 lfc=opt$lfcReq)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
654 sumStatus <- summary(status)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
655
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
656 for (i in 1:length(contrastData)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
diff changeset
657 # Collect counts for differential expression
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
658 upCount[i] <- sumStatus["Up", i]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
659 downCount[i] <- sumStatus["Down", i]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
660 flatCount[i] <- sumStatus["NotSig", i]
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
diff changeset
661
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
662 # Write top expressions table
6
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iuc
parents: 5
diff changeset
663 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
664 top <- topTreat(fit, coef=i, number=Inf, sort.by="P")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
665 } else{
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
666 top <- topTable(fit, coef=i, number=Inf, sort.by="P")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
667 }
4
a61a6e62e91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents: 3
diff changeset
668 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
669
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
670 linkName <- paste0(deMethod, "_", contrastData[i], ".tsv")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
671 linkAddr <- paste0(deMethod, "_", contrastData[i], ".tsv")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
672 linkData <- rbind(linkData, c(linkName, linkAddr))
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
diff changeset
673
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
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parents: 4
diff changeset
674 # Plot MD (log ratios vs mean average) using limma package on weighted
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
675 pdf(mdOutPdf[i])
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
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parents: 4
diff changeset
676 limma::plotMD(fit, status=status[, i], coef=i,
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
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diff changeset
677 main=paste("MD Plot:", unmake.names(contrastData[i])),
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
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diff changeset
678 hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1),
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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parents: 2
diff changeset
679 xlab="Average Expression", ylab="logFC")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
680
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
681 abline(h=0, col="grey", lty=2)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
682
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
683 linkName <- paste0("MDPlot_", contrastData[i], ".pdf")
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
684 linkAddr <- paste0("mdplot_", contrastData[i], ".pdf")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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diff changeset
685 linkData <- rbind(linkData, c(linkName, linkAddr))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
686 invisible(dev.off())
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
687
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
688 # Plot Volcano
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
689 pdf(volOutPdf[i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
690 if (haveAnno) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
691 # labels must be in second column currently
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
692 limma::volcanoplot(fit, coef=i,
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
693 main=paste("Volcano Plot:", unmake.names(contrastData[i])),
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
694 highlight=opt$volhiOpt,
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
695 names=fit$genes[, 2])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
696 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
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diff changeset
697 limma::volcanoplot(fit, coef=i,
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
698 main=paste("Volcano Plot:", unmake.names(contrastData[i])),,
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
699 highlight=opt$volhiOpt,
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
700 names=fit$genes$GeneID)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
701 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
702 linkName <- paste0("VolcanoPlot_", contrastData[i], ".pdf")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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diff changeset
703 linkAddr <- paste0("volplot_", contrastData[i], ".pdf")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
704 linkData <- rbind(linkData, c(linkName, linkAddr))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
705 invisible(dev.off())
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
706
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
707 # PNG of MD and Volcano
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
708 png(mdvolOutPng[i], width=1200, height=600)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
709 par(mfrow=c(1, 2), mar=c(5,4,2,2)+0.1, oma=c(0,0,3,0))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
710 limma::plotMD(fit, status=status[, i], coef=i, main="MD Plot",
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
711 hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1),
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
712 xlab="Average Expression", ylab="logFC")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
713
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
714 abline(h=0, col="grey", lty=2)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
715
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
716 # Volcano plots
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
717 if (haveAnno) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
718 # labels must be in second column currently
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
719 limma::volcanoplot(fit, coef=i, main="Volcano Plot",
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
720 highlight=opt$volhiOpt,
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
721 names=fit$genes[, 2])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
722 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
723 limma::volcanoplot(fit, coef=i, main="Volcano Plot",
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
724 highlight=opt$volhiOpt,
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
725 names=fit$genes$GeneID)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
726 }
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
727
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
728 imgName <- paste0("MDVolPlot_", contrastData[i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
729 imgAddr <- paste0("mdvolplot_", contrastData[i], ".png")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
730 imageData <- rbind(imageData, c(imgName, imgAddr))
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
731 title(paste0("Contrast: ", unmake.names(contrastData[i])), outer=TRUE, cex.main=1.5)
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
732 invisible(dev.off())
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
733 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
734 sigDiff <- data.frame(Up=upCount, Flat=flatCount, Down=downCount)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
735 row.names(sigDiff) <- contrastData
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
736
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
737 # Save relevant items as rda object
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
738 if (wantRda) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
739 print("Saving RData")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
740 if (wantWeight) {
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
741 save(counts, data, y, status, plotData, labels, factors, wts, fit, top, contrasts, design,
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
742 file=rdaOut, ascii=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
743 } else {
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
744 save(counts, data, y, status, plotData, labels, factors, fit, top, contrasts, design,
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
745 file=rdaOut, ascii=TRUE)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
746 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
747 linkData <- rbind(linkData, c((paste0(deMethod, "_analysis.RData")), (paste0(deMethod, "_analysis.RData"))))
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
748 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
749
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
750 # Record session info
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
751 writeLines(capture.output(sessionInfo()), sessionOut)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
752 linkData <- rbind(linkData, c("Session Info", "session_info.txt"))
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
753
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
754 # Record ending time and calculate total run time
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
755 timeEnd <- as.character(Sys.time())
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
756 timeTaken <- capture.output(round(difftime(timeEnd,timeStart), digits=3))
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
757 timeTaken <- gsub("Time difference of ", "", timeTaken, fixed=TRUE)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
758 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
759 ### HTML Generation
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
760 ################################################################################
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
761
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
762 # Clear file
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
763 cat("", file=opt$htmlPath)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
764
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
765 cata("<html>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
766
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
767 cata("<body>\n")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
768 cata("<h3>Limma Analysis Output:</h3>\n")
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
769 cata("Links to PDF copies of plots are in 'Plots' section below <br />\n")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
770
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
771 for (i in 1:nrow(imageData)) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
772 if (grepl("density|box|mdvol", imageData$Link[i])) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
773 HtmlImage(imageData$Link[i], imageData$Label[i], width=1200)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
774 } else if (wantWeight) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
775 HtmlImage(imageData$Link[i], imageData$Label[i], width=1000)
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
776 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
777 HtmlImage(imageData$Link[i], imageData$Label[i])
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
778 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
779 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
780
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
781 cata("<h4>Differential Expression Counts:</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
782
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
783 cata("<table border=\"1\" cellpadding=\"4\">\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
784 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
785 TableItem()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
786 for (i in colnames(sigDiff)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
787 TableHeadItem(i)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
788 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
789 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
790 for (i in 1:nrow(sigDiff)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
791 cata("<tr>\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
792 TableHeadItem(unmake.names(row.names(sigDiff)[i]))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
793 for (j in 1:ncol(sigDiff)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
794 TableItem(as.character(sigDiff[i, j]))
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
795 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
796 cata("</tr>\n")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
797 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
798 cata("</table>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
799
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
800 cata("<h4>Plots:</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
801 for (i in 1:nrow(linkData)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
802 if (grepl(".pdf", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
803 HtmlLink(linkData$Link[i], linkData$Label[i])
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
804 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
805 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
806
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
807 cata("<h4>Tables:</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
808 for (i in 1:nrow(linkData)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
809 if (grepl(".tsv", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
810 HtmlLink(linkData$Link[i], linkData$Label[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
811 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
812 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
813
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
814 if (wantRda) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
815 cata("<h4>R Data Object:</h4>\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
816 for (i in 1:nrow(linkData)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
817 if (grepl(".RData", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
818 HtmlLink(linkData$Link[i], linkData$Label[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
819 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
820 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
821 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
822
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
823 cata("<p>Alt-click links to download file.</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
824 cata("<p>Click floppy disc icon associated history item to download ")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
825 cata("all files.</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
826 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
827
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
828 cata("<h4>Additional Information</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
829 cata("<ul>\n")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
830
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
831 if (filtCPM || filtSmpCount || filtTotCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
832 if (filtCPM) {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
833 tempStr <- paste("Genes without more than", opt$cpmReq,
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
834 "CPM in at least", opt$sampleReq, "samples are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
835 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
836 } else if (filtSmpCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
837 tempStr <- paste("Genes without more than", opt$cntReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
838 "counts in at least", opt$sampleReq, "samples are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
839 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
840 } else if (filtTotCount) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
841 tempStr <- paste("Genes without more than", opt$cntReq,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
842 "counts, after summing counts for all samples, are insignificant",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
843 "and filtered out.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
844 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
845
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
846 ListItem(tempStr)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
847 filterProp <- round(filteredCount/preFilterCount*100, digits=2)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
848 tempStr <- paste0(filteredCount, " of ", preFilterCount," (", filterProp,
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
849 "%) genes were filtered out for low expression.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
850 ListItem(tempStr)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
851 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
852 ListItem(opt$normOpt, " was the method used to normalise library sizes.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
853 if (wantTrend) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
854 ListItem("The limma-trend method was used.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
855 } else {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
856 ListItem("The limma-voom method was used.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
857 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
858 if (wantWeight) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
859 ListItem("Weights were applied to samples.")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
860 } else {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
861 ListItem("Weights were not applied to samples.")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
862 }
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
863 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
864 ListItem(paste("Testing significance relative to a fold-change threshold (TREAT) was performed using a threshold of log2 =", opt$lfcReq, "at FDR of", opt$pValReq, "."))
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
865 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
866 if (wantRobust) {
6
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
867 if (wantTreat) {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
868 ListItem("TREAT was used with robust settings (robust=TRUE).")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
869 } else {
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
870 ListItem("eBayes was used with robust settings (robust=TRUE).")
39fa12a6d885 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents: 5
diff changeset
871 }
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
872 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
873 if (opt$pAdjOpt!="none") {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
874 if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
875 tempStr <- paste0("MD Plot highlighted genes are significant at FDR ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
876 "of ", opt$pValReq," and exhibit log2-fold-change of at ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
877 "least ", opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
878 ListItem(tempStr)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
879 } else if (opt$pAdjOpt=="holm") {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
880 tempStr <- paste0("MD Plot highlighted genes are significant at adjusted ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
881 "p-value of ", opt$pValReq," by the Holm(1979) ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
882 "method, and exhibit log2-fold-change of at least ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
883 opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
884 ListItem(tempStr)
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
885 }
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
886 } else {
5
d8a55b5f0de0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents: 4
diff changeset
887 tempStr <- paste0("MD Plot highlighted genes are significant at p-value ",
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
888 "of ", opt$pValReq," and exhibit log2-fold-change of at ",
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
889 "least ", opt$lfcReq, ".")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
890 ListItem(tempStr)
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
891 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
892 cata("</ul>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
893
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
894 cata("<h4>Summary of experimental data:</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
895
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
896 cata("<p>*CHECK THAT SAMPLES ARE ASSOCIATED WITH CORRECT GROUP(S)*</p>\n")
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
897
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
898 cata("<table border=\"1\" cellpadding=\"3\">\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
899 cata("<tr>\n")
1
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
900 TableHeadItem("SampleID")
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
901 TableHeadItem(names(factors)[1]," (Primary Factor)")
76d01fe0ec36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents: 0
diff changeset
902
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
903 if (ncol(factors) > 1) {
2
a330ddf43861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents: 1
diff changeset
904 for (i in names(factors)[2:length(names(factors))]) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
905 TableHeadItem(i)
2
a330ddf43861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents: 1
diff changeset
906 }
a330ddf43861 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents: 1
diff changeset
907 cata("</tr>\n")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
908 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
909
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
910 for (i in 1:nrow(factors)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
911 cata("<tr>\n")
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
912 TableHeadItem(row.names(factors)[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
913 for (j in 1:ncol(factors)) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
914 TableItem(as.character(unmake.names(factors[i, j])))
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
915 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
916 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
917 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
918 cata("</table>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
919
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
920 cit <- character()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
921 link <- character()
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
922 link[1] <- paste0("<a href=\"",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
923 "http://www.bioconductor.org/packages/release/bioc/",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
924 "vignettes/limma/inst/doc/usersguide.pdf",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
925 "\">", "limma User's Guide", "</a>.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
926
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
927 link[2] <- paste0("<a href=\"",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
928 "http://www.bioconductor.org/packages/release/bioc/",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
929 "vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
930 "\">", "edgeR User's Guide", "</a>")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
931
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
932 cit[1] <- paste("Please cite the following paper for this tool:")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
933
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
934 cit[2] <- paste("Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME,",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
935 "Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? ",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
936 "Modelling sample and observational level variability improves power ",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
937 "in RNA-seq analyses. Nucleic Acids Research, 43(15), e97.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
938
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
939 cit[3] <- paste("Please cite the paper below for the limma software itself.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
940 "Please also try to cite the appropriate methodology articles",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
941 "that describe the statistical methods implemented in limma,",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
942 "depending on which limma functions you are using. The",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
943 "methodology articles are listed in Section 2.1 of the",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
944 link[1],
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
945 "Cite no. 3 only if sample weights were used.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
946 cit[4] <- paste("Smyth GK (2005). Limma: linear models for microarray data.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
947 "In: 'Bioinformatics and Computational Biology Solutions using",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
948 "R and Bioconductor'. R. Gentleman, V. Carey, S. doit,.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
949 "Irizarry, W. Huber (eds), Springer, New York, pages 397-420.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
950 cit[5] <- paste("Please cite the first paper for the software itself and the",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
951 "other papers for the various original statistical methods",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
952 "implemented in edgeR. See Section 1.2 in the", link[2],
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
953 "for more detail.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
954 cit[6] <- paste("Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
955 "Bioconductor package for differential expression analysis",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
956 "of digital gene expression data. Bioinformatics 26, 139-140")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
957 cit[7] <- paste("Robinson MD and Smyth GK (2007). Moderated statistical tests",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
958 "for assessing differences in tag abundance. Bioinformatics",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
959 "23, 2881-2887")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
960 cit[8] <- paste("Robinson MD and Smyth GK (2008). Small-sample estimation of",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
961 "negative binomial dispersion, with applications to SAGE data.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
962 "Biostatistics, 9, 321-332")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
963 cit[9] <- paste("McCarthy DJ, Chen Y and Smyth GK (2012). Differential",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
964 "expression analysis of multifactor RNA-Seq experiments with",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
965 "respect to biological variation. Nucleic Acids Research 40,",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
966 "4288-4297")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
967 cit[10] <- paste("Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
968 "precision weights unlock linear model analysis tools for",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
969 "RNA-seq read counts. Genome Biology 15, R29.")
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
970 cit[11] <- paste("Ritchie ME, Diyagama D, Neilson J, van Laar R,",
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
971 "Dobrovic A, Holloway A and Smyth GK (2006).",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
972 "Empirical array quality weights for microarray data.",
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
973 "BMC Bioinformatics 7, Article 261.")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
974 cata("<h3>Citations</h3>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
975 cata(cit[1], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
976 cata("<br>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
977 cata(cit[2], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
978
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
979 cata("<h4>limma</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
980 cata(cit[3], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
981 cata("<ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
982 ListItem(cit[4])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
983 ListItem(cit[10])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
984 ListItem(cit[11])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
985 cata("</ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
986
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
987 cata("<h4>edgeR</h4>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
988 cata(cit[5], "\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
989 cata("<ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
990 ListItem(cit[6])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
991 ListItem(cit[7])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
992 ListItem(cit[8])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
993 ListItem(cit[9])
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
994 cata("</ol>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
995
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
996 cata("<p>Please report problems or suggestions to: su.s@wehi.edu.au</p>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
997
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
998 for (i in 1:nrow(linkData)) {
3
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
999 if (grepl("session_info", linkData$Link[i])) {
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1000 HtmlLink(linkData$Link[i], linkData$Label[i])
38aab66ae5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents: 2
diff changeset
1001 }
0
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1002 }
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1003
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1004 cata("<table border=\"0\">\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1005 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1006 TableItem("Task started at:"); TableItem(timeStart)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1007 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1008 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1009 TableItem("Task ended at:"); TableItem(timeEnd)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1010 cata("</tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1011 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1012 TableItem("Task run time:"); TableItem(timeTaken)
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1013 cata("<tr>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1014 cata("</table>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1015
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1016 cata("</body>\n")
bdebdea5f6a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff changeset
1017 cata("</html>")