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| author | devteam |
|---|---|
| date | Fri, 18 Dec 2015 18:53:41 -0500 |
| parents | d1521b82b9fe |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="compute_q_values" name="Compute q-values" version="1.0.1"> |
| 2 <description>based on multiple simultaneous tests p-values</description> | |
| 1 | 3 <requirements> |
| 4 <requirement type="package" version="2.11.0">R</requirement> | |
| 5 <requirement type="package" version="1.34.0">bioc_qvalue</requirement> | |
| 6 </requirements> | |
| 0 | 7 <command interpreter="perl"> |
| 8 compute_q_values.pl $inputFile1 $inputLambda2 $inputPI0_method3 $inputFDR_level4 $inputRobust5 $outputFile1 $outputFile2 | |
| 9 </command> | |
| 10 | |
| 11 <inputs> | |
| 12 <param format="tabular" name="inputFile1" type="data" label="Select the p-values file"/> | |
| 13 | |
|
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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14 <param type="text" name="inputLambda2" 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"/> |
| 0 | 15 |
| 16 <param name="inputPI0_method3" type="select" label="Choose the PI method:"> | |
| 17 <option value="smoother">smoother</option> | |
| 18 <option value="bootstrap">bootstrap</option> | |
| 19 </param> | |
| 20 | |
|
3
d1521b82b9fe
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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21 <param type="float" name="inputFDR_level4" value="" label="What is the FDR level?" help="The FDR level must be between 0 and 1"/> |
| 0 | 22 |
| 23 <param name="inputRobust5" type="select" label="Do you want to make the estimate more robust:" help="Choose TRUE for small p-values"> | |
| 24 <option value="FALSE">FALSE</option> | |
| 25 <option value="TRUE">TRUE</option> | |
| 26 </param> | |
| 27 </inputs> | |
| 28 | |
| 29 <outputs> | |
| 30 <data format="tabular" name="outputFile1"/> | |
| 31 <data format="pdf" name="outputFile2"/> | |
| 32 </outputs> | |
| 33 | |
| 34 <tests> | |
| 35 <test> | |
| 36 <param name="inputFile1" value="p_values.tabular" ftype="tabular" /> | |
| 37 <param name="inputLambda2" value="sequence_from_0_to_0.95_increment_0.05" /> | |
| 38 <param name="inputPI0_method3" value="smoother" /> | |
| 39 <param name="inputFDR_level4" value="0.05" /> | |
| 40 <param name="inputRobust5" value="FALSE" /> | |
| 41 <output name="outputFile1" file="q_values.tabular" /> | |
| 42 <output name="outputFile1" file="p_q_hists_Q_plots.pdf" /> | |
| 43 </test> | |
| 44 </tests> | |
| 45 | |
| 46 <help> | |
| 47 | |
| 48 .. class:: infomark | |
| 49 | |
| 50 **What it does** | |
| 51 | |
| 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: | |
| 53 | |
| 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. | |
| 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. | |
| 56 - The third input is PI method which is either "smoother" or "bootstrap". | |
| 57 - The fourth input is the FDR (false discovery rate) level which is a decimal number between 0.0 and 1.0. | |
| 58 - The fifth input is either TRUE or FALSE for the estimate robustness. | |
| 59 | |
| 60 The program gives two outputs: | |
| 61 | |
| 62 - The first output is a TABULAR format file consisting of three columns: | |
| 63 | |
| 64 - the left column represents the p-values of multiple simultaneous tests, one line for every p-value | |
| 65 - the middle column represents the q-values corresponding to the p-values | |
| 66 - the third column represent the significance values, either 1 for significant or 0 for non-significant | |
| 67 | |
| 68 - The second output is a PDF format file consisting of three pages: | |
| 69 | |
| 70 - the first page represents the p-values histogram | |
| 71 - the second page represents the q-values histogram | |
| 72 - the third page represents the four Q-plots as introduced in the "qvalue" package manual. | |
| 73 | |
| 74 | |
| 75 **Example** | |
| 76 | |
| 77 Let us have the first input file of p-values as follows:: | |
| 78 | |
| 79 0.140627492 | |
| 80 0.432249886 | |
| 81 0.122120877 | |
| 82 0.142010182 | |
| 83 0.012909858 | |
| 84 0.000142807 | |
| 85 0.039841941 | |
| 86 0.035173303 | |
| 87 0.011340057 | |
| 88 1.01E-05 | |
| 89 0.212738282 | |
| 90 0.091256284 | |
| 91 0.547375415 | |
| 92 0.189589833 | |
| 93 6.18E-12 | |
| 94 0.001235875 | |
| 95 1.10E-05 | |
| 96 9.75E-07 | |
| 97 2.13E-18 | |
| 98 2.54E-16 | |
| 99 1.20E-19 | |
| 100 9.76E-14 | |
| 101 0.359181534 | |
| 102 0.03661672 | |
| 103 0.400459987 | |
| 104 0.387436466 | |
| 105 0.342075061 | |
| 106 0.904129283 | |
| 107 0.031152635 | |
| 108 | |
| 109 Running the program will give the following output:: | |
| 110 | |
| 111 pi0: 0.140311054 | |
| 112 | |
| 113 FDR level: 0.05 | |
| 114 | |
| 115 p-value q-value significant | |
| 116 0.1406275 0.02889212 1 | |
| 117 0.4322499 0.06514199 0 | |
| 118 0.1221209 0.02760624 1 | |
| 119 0.1420102 0.02889212 1 | |
| 120 0.01290986 0.00437754 1 | |
| 121 0.000142807 6.46E-05 1 | |
| 122 0.03984194 0.01013235 1 | |
| 123 0.0351733 0.009932946 1 | |
| 124 0.01134006 0.004194811 1 | |
| 125 1.01E-05 5.59E-06 1 | |
| 126 0.2127383 0.03934711 1 | |
| 127 0.09125628 0.02184257 1 | |
| 128 0.5473754 0.07954578 0 | |
| 129 0.1895898 0.03673547 1 | |
| 130 6.18E-12 5.03E-12 1 | |
| 131 0.001235875 0.00050288 1 | |
| 132 1.10E-05 5.59E-06 1 | |
| 133 9.75E-07 6.61E-07 1 | |
| 134 2.13E-18 4.33E-18 1 | |
| 135 2.54E-16 3.45E-16 1 | |
| 136 1.20E-19 4.88E-19 1 | |
| 137 9.76E-14 9.93E-14 1 | |
| 138 0.3591815 0.06089654 0 | |
| 139 0.03661672 0.009932946 1 | |
| 140 0.40046 0.0626723 0 | |
| 141 0.3874365 0.0626723 0 | |
| 142 0.3420751 0.06051785 0 | |
| 143 0.9041293 0.1268593 0 | |
| 144 0.03115264 0.009750824 1 | |
| 145 | |
| 146 | |
| 2 | 147 .. image:: p_hist.png |
| 0 | 148 |
| 149 | |
| 2 | 150 .. image:: q_hist.png |
| 0 | 151 |
| 152 | |
| 2 | 153 .. image:: Q_plots.png |
| 0 | 154 |
| 155 | |
| 156 </help> | |
| 157 | |
| 158 </tool> |