Mercurial > repos > artbio > gsc_mannwhitney_de

annotate MannWhitney_DE.R @ 0:c67dba545a37 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
author artbio
date Mon, 24 Jun 2019 13:39:39 -0400
parents
children 3d86c89f15bf
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0
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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1 ####################
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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2 # Differential #
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3 # analysis #
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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4 ####################
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5
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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6 # Perform a differential analysis between 2
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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7 # groups of cells.
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8
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9 # Example of command
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10 # Rscript MannWhitney_DE.R --input <input.tsv> --sep <tab> --colnames <TRUE> --metadata <signature.tsv> --column_name <rate> --fdr <0.01> --output <diff_analysis.tsv>
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11
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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12 # load packages that are provided in the conda env
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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13 options( show.error.messages=F,
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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14 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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15 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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16 warnings()
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17 library(optparse)
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18
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19 #Arguments
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20 option_list = list(
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21 make_option(
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22 "--input",
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23 default = NA,
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24 type = 'character',
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25 help = "Input file that contains log2(CPM +1) values"
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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26 ),
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27 make_option(
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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28 "--sep",
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29 default = '\t',
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30 type = 'character',
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31 help = "File separator [default : '%default' ]"
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32 ),
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33 make_option(
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34 "--colnames",
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35 default = TRUE,
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36 type = 'logical',
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37 help = "Consider first line as header ? [default : '%default' ]"
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38 ),
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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39 make_option(
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40 "--comparison_factor_file",
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41 default = NA,
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42 type = 'character',
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43 help = " A two column table : cell identifiers and a comparison factor that split cells in two categories (high/low, HOM/HET,...)"
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44 ),
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45 make_option(
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46 "--factor1",
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47 type = 'character',
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48 help = "level associated to the control condition in the factor file"
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49 ),
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50 make_option(
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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51 "--factor2",
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52 type = 'character',
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53 help = "level associated to the test condition in the factor file"
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54 ),
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55 make_option(
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56 "--fdr",
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57 default = 0.01,
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58 type = 'numeric',
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59 help = "FDR threshold [default : '%default' ]"
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60 ),
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61 make_option(
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62 "--log",
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63 default=FALSE,
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64 action="store_true",
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65 type = 'logical',
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66 help = "Expression data are log-transformed [default : '%default' ]"
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67 ),
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68 make_option(
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69 "--output",
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70 default = "results.tsv",
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71 type = 'character',
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72 help = "Output name [default : '%default' ]"
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73 )
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74 )
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75
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76 opt = parse_args(OptionParser(option_list = option_list),
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77 args = commandArgs(trailingOnly = TRUE))
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78
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79 if (opt$sep == "tab") {opt$sep = "\t"}
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80 if (opt$sep == "comma") {opt$sep = ","}
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81
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82 #Open files
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83 data.counts <- read.table(
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84 opt$input,
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85 h = opt$colnames,
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86 row.names = 1,
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87 sep = opt$sep,
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88 check.names = F
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89 )
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90
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91 metadata <- read.table(
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92 opt$comparison_factor_file,
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93 header = TRUE,
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94 stringsAsFactors = F,
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95 sep = "\t",
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96 check.names = FALSE,
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97 row.names = 1
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98 )
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99
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100 metadata <- subset(metadata, rownames(metadata) %in% colnames(data.counts))
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101
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102 # Create two logical named vectors for each factor level of cell signature
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103 factor1_cells <- setNames(metadata[,1] == opt$factor1, rownames(metadata))
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104 factor2_cells <- setNames(metadata[,1] == opt$factor2, rownames(metadata))
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105
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106 ## Mann-Whitney test (Two-sample Wilcoxon test)
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107 MW_test <- data.frame(t(apply(data.counts, 1, function(x) {
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108 do.call("cbind", wilcox.test(x[names(factor1_cells)[factor1_cells]], x[names(factor2_cells)[factor2_cells]]))[, 1:2]
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109 })), stringsAsFactors = F)
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110
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111 # Benjamini-Hochberg correction and significativity
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112 MW_test$p.adjust <- p.adjust(as.numeric(MW_test$p.value), method = "BH" , n = nrow(MW_test))
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113 # MW_test$Critical.value <- (rank(MW_test$p.value) / nrow(MW_test)) * opt$fdr
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114 MW_test$Significant <- MW_test$p.adjust < opt$fdr
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115
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116 ## Descriptive Statistics Function
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117 descriptive_stats <- function(InputData) {
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118 SummaryData = data.frame(
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119 mean = rowMeans(InputData),
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120 SD = apply(InputData, 1, sd),
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121 Variance = apply(InputData, 1, var),
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122 Percentage_Detection = apply(InputData, 1, function(x, y = InputData) {
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123 (sum(x != 0) / ncol(y)) * 100
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124 }),
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125 mean_condition2 = rowMeans(InputData[,factor2_cells]),
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126 mean_condition1 = rowMeans(InputData[, factor1_cells])
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127 )
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128 if(opt$log) {
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129 SummaryData$log2FC <- SummaryData$mean_condition2 - SummaryData$mean_condition1
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130 } else {
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131 SummaryData$log2FC <- log2(SummaryData$mean_condition2 / SummaryData$mean_condition1)
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132 }
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133 return(SummaryData)
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134 }
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135
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136 gene_stats <- descriptive_stats(data.counts)
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137
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138 results <- merge(gene_stats, MW_test, by = "row.names")
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139 colnames(results)[1] <- "genes"
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140
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141 # Save files
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142 write.table(
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143 results,
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144 opt$output,
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145 sep = "\t",
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146 quote = F,
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147 col.names = T,
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148 row.names = F
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149 )