Mercurial > repos > artbio > gsc_cpm_tpm_rpk

annotate cpm_tpm_rpk.R @ 1:46507a10106c draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 06c8d40814f68cbf4d24b2ea70a11407bc40d072
author artbio
date Mon, 24 Jun 2019 19:15:51 -0400
parents ce3d027ec26b
children
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ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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1 if (length(commandArgs(TRUE)) == 0) {
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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2 system("Rscript cpm_tpm_rpk.R -h", intern = F)
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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3 q("no")
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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4 }
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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5
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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6
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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7 # load packages that are provided in the conda env
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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8 options( show.error.messages=F,
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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9 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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11 warnings()
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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12 library(optparse)
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13
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14 #Arguments
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15 option_list = list(
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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16 make_option(
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17 c("-d", "--data"),
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18 default = NA,
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19 type = 'character',
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20 help = "Input file that contains count values to transform"
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21 ),
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22 make_option(
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23 c("-t", "--type"),
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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24 default = 'cpm',
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25 type = 'character',
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26 help = "Transformation type, either cpm, tpm, rpk or none[default : '%default' ]"
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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27 ),
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28 make_option(
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29 c("-s", "--sep"),
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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30 default = '\t',
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31 type = 'character',
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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32 help = "File separator [default : '%default' ]"
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33 ),
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34 make_option(
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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35 c("-c", "--colnames"),
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36 default = TRUE,
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37 type = 'logical',
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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38 help = "Consider first line as header ? [default : '%default' ]"
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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39 ),
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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40 make_option(
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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41 c("-f", "--gene"),
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42 default = NA,
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43 type = 'character',
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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44 help = "Two column of gene length file"
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45 ),
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46 make_option(
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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47 c("-a", "--gene_sep"),
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48 default = '\t',
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49 type = 'character',
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50 help = "Gene length file separator [default : '%default' ]"
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51 ),
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52 make_option(
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53 c("-b", "--gene_header"),
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54 default = TRUE,
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55 type = 'logical',
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56 help = "Consider first line of gene length as header ? [default : '%default' ]"
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57 ),
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58 make_option(
ce3d027ec26b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_cpm_tpm_rpk commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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59 c("-l", "--log"),
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60 default = FALSE,
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61 type = 'logical',
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62 help = "Should be log transformed as well ? (log2(data +1)) [default : '%default' ]"
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63 ),
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64 make_option(
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65 c("-o", "--out"),
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66 default = "res.tab",
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67 type = 'character',
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68 help = "Output name [default : '%default' ]"
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69 )
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70 )
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71
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72 opt = parse_args(OptionParser(option_list = option_list),
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73 args = commandArgs(trailingOnly = TRUE))
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74
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75 if (opt$sep == "tab") {opt$sep = "\t"}
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76 if (opt$gene_sep == "tab") {opt$gene_sep = "\t"}
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77
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78 cpm <- function(count) {
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79 t(t(count) / colSums(count)) * 1000000
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80 }
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81
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82
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83 rpk <- function(count, length) {
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84 count / (length / 1000)
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85 }
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86
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87 tpm <- function(count, length) {
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artbio
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88 RPK = rpk(count, length)
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artbio
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89 perMillion_factor = colSums(RPK) / 1000000
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artbio
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90 TPM = RPK / perMillion_factor
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artbio
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91 return(TPM)
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artbio
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92 }
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93
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artbio
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94 data = read.table(
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artbio
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95 opt$data,
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artbio
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96 check.names = FALSE,
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artbio
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97 header = opt$colnames,
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artbio
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98 row.names = 1,
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artbio
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99 sep = opt$sep
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artbio
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100 )
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101
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artbio
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102 if (opt$type == "tpm" | opt$type == "rpk") {
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artbio
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103 gene_length = as.data.frame(
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artbio
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104 read.table(
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artbio
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105 opt$gene,
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artbio
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106 h = opt$gene_header,
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artbio
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107 row.names = 1,
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artbio
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108 sep = opt$gene_sep
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109 )
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artbio
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110 )
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artbio
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111 gene_length = as.data.frame(gene_length[match(rownames(data), rownames(gene_length)), ], rownames(data))
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112 }
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113
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114
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115 if (opt$type == "cpm")
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artbio
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116 res = cpm(data)
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artbio
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117 if (opt$type == "tpm")
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artbio
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118 res = as.data.frame(apply(data, 2, tpm, length = gene_length), row.names = rownames(data))
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119 if (opt$type == "rpk")
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artbio
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120 res = as.data.frame(apply(data, 2, rpk, length = gene_length), row.names = rownames(data))
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artbio
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121 if (opt$type == "none")
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artbio
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122 res = data
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artbio
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123 colnames(res) = colnames(data)
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124
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125
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126 if (opt$log == TRUE) {
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artbio
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127 res = log2(res + 1)
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128 }
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129
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artbio
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130 write.table(
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artbio
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131 cbind(Genes = rownames(res), res),
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artbio
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132 opt$out,
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artbio
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133 col.names = opt$colnames,
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artbio
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134 row.names = F,
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artbio
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135 quote = F,
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artbio
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136 sep = "\t"
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artbio
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137 )
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138
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139
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140
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141
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142
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143
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144
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145
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146
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147
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148
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149