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