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1 <tool id="compute_q_values" name="Compute q-values" version="1.0.1">
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2 <description>based on multiple simultaneous tests p-values</description>
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1
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3 <requirements>
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4 <requirement type="package" version="2.11.0">R</requirement>
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5 <requirement type="package" version="1.34.0">bioc_qvalue</requirement>
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6 </requirements>
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0
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7 <command interpreter="perl">
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8 compute_q_values.pl $inputFile1 $inputLambda2 $inputPI0_method3 $inputFDR_level4 $inputRobust5 $outputFile1 $outputFile2
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9 </command>
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10
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11 <inputs>
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12 <param format="tabular" name="inputFile1" type="data" label="Select the p-values file"/>
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13
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14 <param type="text" name="inputLambda2" size="100" value="sequence_from_0_to_0.95_increment_0.05" label="What is the lambda value?" help="Either choose the default sequence or one deciaml value between 0 and 1"/>
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15
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16 <param name="inputPI0_method3" type="select" label="Choose the PI method:">
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17 <option value="smoother">smoother</option>
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18 <option value="bootstrap">bootstrap</option>
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19 </param>
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20
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21 <param type="float" name="inputFDR_level4" size="5" value="" label="What is the FDR level?" help="The FDR level must be between 0 and 1"/>
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22
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23 <param name="inputRobust5" type="select" label="Do you want to make the estimate more robust:" help="Choose TRUE for small p-values">
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24 <option value="FALSE">FALSE</option>
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25 <option value="TRUE">TRUE</option>
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26 </param>
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27 </inputs>
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28
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29 <outputs>
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30 <data format="tabular" name="outputFile1"/>
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31 <data format="pdf" name="outputFile2"/>
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32 </outputs>
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33
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34 <tests>
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35 <test>
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36 <param name="inputFile1" value="p_values.tabular" ftype="tabular" />
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37 <param name="inputLambda2" value="sequence_from_0_to_0.95_increment_0.05" />
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38 <param name="inputPI0_method3" value="smoother" />
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39 <param name="inputFDR_level4" value="0.05" />
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40 <param name="inputRobust5" value="FALSE" />
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41 <output name="outputFile1" file="q_values.tabular" />
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42 <output name="outputFile1" file="p_q_hists_Q_plots.pdf" />
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43 </test>
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44 </tests>
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45
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46 <help>
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47
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48 .. class:: infomark
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49
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50 **What it does**
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51
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52 This program computes the q-values based on the p-values of multiple simultaneous tests. The q-values are computed using a specific R package, created by John Storey and Alan Dabney, called "qvalue". The program takes five inputs:
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53
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54 - The first input is a TABULAR format file consisting of one column only that represents the p-values of multiple simultaneous tests, one line for every p-value.
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55 - The second input is the lambda parameter. The user can choose either the default: seq(0, 0.95, 0.05) or a decimal number between 0.0 and 1.0.
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56 - The third input is PI method which is either "smoother" or "bootstrap".
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57 - The fourth input is the FDR (false discovery rate) level which is a decimal number between 0.0 and 1.0.
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58 - The fifth input is either TRUE or FALSE for the estimate robustness.
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59
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60 The program gives two outputs:
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61
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62 - The first output is a TABULAR format file consisting of three columns:
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63
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64 - the left column represents the p-values of multiple simultaneous tests, one line for every p-value
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65 - the middle column represents the q-values corresponding to the p-values
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66 - the third column represent the significance values, either 1 for significant or 0 for non-significant
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67
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68 - The second output is a PDF format file consisting of three pages:
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69
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70 - the first page represents the p-values histogram
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71 - the second page represents the q-values histogram
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72 - the third page represents the four Q-plots as introduced in the "qvalue" package manual.
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73
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74
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75 **Example**
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76
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77 Let us have the first input file of p-values as follows::
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78
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79 0.140627492
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80 0.432249886
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81 0.122120877
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82 0.142010182
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83 0.012909858
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84 0.000142807
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85 0.039841941
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86 0.035173303
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87 0.011340057
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88 1.01E-05
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89 0.212738282
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90 0.091256284
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91 0.547375415
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92 0.189589833
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93 6.18E-12
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94 0.001235875
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95 1.10E-05
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96 9.75E-07
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97 2.13E-18
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98 2.54E-16
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99 1.20E-19
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100 9.76E-14
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101 0.359181534
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102 0.03661672
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103 0.400459987
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104 0.387436466
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105 0.342075061
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106 0.904129283
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107 0.031152635
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108
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109 Running the program will give the following output::
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110
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111 pi0: 0.140311054
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112
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113 FDR level: 0.05
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114
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115 p-value q-value significant
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116 0.1406275 0.02889212 1
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117 0.4322499 0.06514199 0
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118 0.1221209 0.02760624 1
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119 0.1420102 0.02889212 1
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120 0.01290986 0.00437754 1
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121 0.000142807 6.46E-05 1
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122 0.03984194 0.01013235 1
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123 0.0351733 0.009932946 1
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124 0.01134006 0.004194811 1
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125 1.01E-05 5.59E-06 1
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126 0.2127383 0.03934711 1
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127 0.09125628 0.02184257 1
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128 0.5473754 0.07954578 0
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129 0.1895898 0.03673547 1
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130 6.18E-12 5.03E-12 1
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131 0.001235875 0.00050288 1
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132 1.10E-05 5.59E-06 1
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133 9.75E-07 6.61E-07 1
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134 2.13E-18 4.33E-18 1
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135 2.54E-16 3.45E-16 1
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136 1.20E-19 4.88E-19 1
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137 9.76E-14 9.93E-14 1
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138 0.3591815 0.06089654 0
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139 0.03661672 0.009932946 1
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140 0.40046 0.0626723 0
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141 0.3874365 0.0626723 0
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142 0.3420751 0.06051785 0
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143 0.9041293 0.1268593 0
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144 0.03115264 0.009750824 1
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145
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146
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2
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147 .. image:: p_hist.png
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148
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149
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150 .. image:: q_hist.png
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151
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152
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153 .. image:: Q_plots.png
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154
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155
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156 </help>
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157
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158 </tool>
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