Mercurial > repos > artbio > gsc_mannwhitney_de

annotate mannwhitney_de.xml @ 2:60964af87364 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 9d570db083bd51751f4784dc367ee18aa0024ecd
author artbio
date Mon, 01 Jul 2019 09:05:28 -0400
parents aef09ac6d0a5
children 3d86c89f15bf
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2
60964af87364 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 9d570db083bd51751f4784dc367ee18aa0024ecd
artbio
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1 <tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.2">
0
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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2 <description>using a Mann-Whitney test</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
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5 </requirements>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript $__tool_directory__/MannWhitney_DE.R
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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11 --input '$input'
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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12 --sep
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13 #if $sep == 'tab':
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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14 'tab'
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15 #elif $sep == 'comma':
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16 'comma'
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17 #end if
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18 --colnames '$colnames'
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19 --factor1 '$factor1'
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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20 --factor2 '$factor2'
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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21 --comparison_factor_file '$comparison_factor_file'
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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22 --fdr '$fdr'
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23 $log
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24 --output '$output'
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25 ]]></command>
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26 <inputs>
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27 <param name="input" type="data" format="txt,tabular" label="Expression data" help="a csv or tsv table file" />
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28 <param name="sep" type="select" label="Indicate column separator">
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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29 <option value="tab" selected="true">Tabs</option>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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30 <option value="comma">Comma</option>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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31 </param>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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32 <param name="colnames" type="select" label="Firt row contains column names">
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33 <option value="TRUE" selected="true">Yes</option>
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34 <option value="FALSE">No</option>
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35 </param>
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36 <param name="comparison_factor_file" type="data" format="tabular" label="Comparison factor table"
2
60964af87364 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 9d570db083bd51751f4784dc367ee18aa0024ecd
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37 help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories.
60964af87364 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 9d570db083bd51751f4784dc367ee18aa0024ecd
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38 Other columns are ignored" />
0
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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39 <param name="factor1" type="text" label="Condition-1. The first level (value) that the comparison factor can take." help="typical values could be 'LOW', 'wt', 't1', etc."/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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40 <param name="factor2" type="text" label="Condition-2. The second level (value) that the comparison factor can take." help="typical values could be 'HIGH', 'mutant', 't2', etc."/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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41 <param name="fdr" type="float" value="0.01" label="FDR threshold"
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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42 help="Reject H0 of no differential expression if adjusted p-values (Benjamini-Hochberg correction) is higher than the FDR cut-off."/>
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43 <param name="log" type="boolean" checked="false" label="Expression data are log-transformed" truevalue="--log" falsevalue=""/>
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44
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45 </inputs>
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46 <outputs>
1
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47 <data name="output" format="tabular" label="Results of Mann-Whitney differential analysis of ${on_string}" />
0
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="input" value="filtered-0.05.tab" ftype="txt"/>
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52 <param name="sep" value="tab" />
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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53 <param name="colnames" value="TRUE"/>
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54 <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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55 <param name="factor1" value="LOW"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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56 <param name="factor2" value="HIGH"/>
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57 <param name="fdr" value="0.01"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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58 <param name="log" value="true"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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59 <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/>
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60 </test>
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61 <test>
2
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62 <param name="input" value="filtered-0.05.tab" ftype="txt"/>
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63 <param name="sep" value="tab" />
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64 <param name="colnames" value="TRUE"/>
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65 <param name="comparison_factor_file" value="signature_3columns.tsv" ftype="tabular"/>
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66 <param name="factor1" value="LOW"/>
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67 <param name="factor2" value="HIGH"/>
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68 <param name="fdr" value="0.01"/>
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69 <param name="log" value="true"/>
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70 <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/>
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71 </test>
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72 <test>
0
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73 <param name="input" value="filterCells_100.tsv" ftype="txt"/>
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74 <param name="sep" value="tab" />
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75 <param name="colnames" value="TRUE"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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76 <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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77 <param name="factor1" value="LOW"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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78 <param name="factor2" value="HIGH"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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79 <param name="fdr" value="0.01"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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80 <param name="log" value="false"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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81 <output name="output" file="geneMetadata_nolog.tsv" ftype="tabular"/>
c67dba545a37 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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82 </test>
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83 </tests>
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84 <help>
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85
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86 **What it does**
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87
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88 The tools takes a table of gene expression values (e.E. log2(CPM+1), etc...) from single cell RNAseq sequencing libraries (columns)
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89
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90 and a metadata file that contains at least two columns :
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91 * Cell identifiers
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92 * A Column that differentiates cell in two groups (the two levels of a comparison factor). It must be a column with only values (the factor levels).
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93
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94 For each gene (rows in expression data file), this script perform a 2-sided Mann-Whitney test between
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95 the two groups of cells (high/low, mutant/wild type) and then adjust the returned p-values by using the
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96 Benjamini-Hochberg (BH) correction. A False Discovery Rate (FDR) threshold is used to determine if gene expression
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97 can be considered as significantly deviant for the H0 hypothesis of no-differential-expression (p-adjust below FDR cut-off) or not (p-adjust above the FDR cut-off).
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98
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99 .. class:: warningmark
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100
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101 **Comparison plan**
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102
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103 Note that log2Fold-Changes computed by the tool are based on the comparison of condition-2 (level-2) versus condition-1 (level-1) i.e.
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104 the tools returns the log2FC in condition-2 **relative** to condition-1.
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105
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106 **Output**
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107
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108 The tools returns a result table. For each row (genes) :
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109
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110 ==================== ======================================================================================================
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111 Column Description
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112 -------------------- ------------------------------------------------------------------------------------------------------
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113 mean mean expression across all cells
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114 SD standard deviation of its expression across all cells
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115 variance variance of expression across all cells
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116 Percentage_detection (number of cells where the gene is detected (expression value superior to 0) / number of cells) * 100
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117 mean_factor2 mean expression across cells of the second group (of log transformed expression values)
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118 mean_factor1 mean expression across cells of the first group (of log transformed expression values)
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119 fold_change mean_factor1 - mean_factor2 (difference of log)
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120 statistic W statistic of Mann-Whitney test
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121 p.value p-value of Mann-Whitney test
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122 p.adjust p-values adjusted from the BH correction
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123 Significant TRUE/FALSE vector (if p-adjust inferior to FDR cut-off then the value is TRUE)
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124 ==================== ======================================================================================================
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125
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126 </help>
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127 <citations>
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128 <citation type="bibtex">
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129 @Manual{,
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130 title = {R: A Language and Environment for Statistical Computing},
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131 author = {{R Core Team}},
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132 organization = {R Foundation for Statistical Computing},
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133 address = {Vienna, Austria},
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134 year = {2014},
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135 url = {http://www.R-project.org/},
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136 }
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137 </citation>
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138 </citations>
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139 </tool>