[2] | 1 | <tool id="compute_q_values" name="Compute q-values" version="1.0.0"> |
---|
| 2 | <description>based on multiple simultaneous tests p-values</description> |
---|
| 3 | |
---|
| 4 | <command interpreter="perl"> |
---|
| 5 | compute_q_values.pl $inputFile1 $inputLambda2 $inputPI0_method3 $inputFDR_level4 $inputRobust5 $outputFile1 $outputFile2 |
---|
| 6 | </command> |
---|
| 7 | |
---|
| 8 | <inputs> |
---|
| 9 | <param format="tabular" name="inputFile1" type="data" label="Select the p-values file"/> |
---|
| 10 | |
---|
| 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"/> |
---|
| 12 | |
---|
| 13 | <param name="inputPI0_method3" type="select" label="Choose the PI method:"> |
---|
| 14 | <option value="smoother">smoother</option> |
---|
| 15 | <option value="bootstrap">bootstrap</option> |
---|
| 16 | </param> |
---|
| 17 | |
---|
| 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"/> |
---|
| 19 | |
---|
| 20 | <param name="inputRobust5" type="select" label="Do you want to make the estimate more robust:" help="Choose TRUE for small p-values"> |
---|
| 21 | <option value="FALSE">FALSE</option> |
---|
| 22 | <option value="TRUE">TRUE</option> |
---|
| 23 | </param> |
---|
| 24 | </inputs> |
---|
| 25 | |
---|
| 26 | <outputs> |
---|
| 27 | <data format="tabular" name="outputFile1"/> |
---|
| 28 | <data format="pdf" name="outputFile2"/> |
---|
| 29 | </outputs> |
---|
| 30 | |
---|
| 31 | <tests> |
---|
| 32 | <test> |
---|
| 33 | <param name="inputFile1" value="p_values.tabular" ftype="tabular" /> |
---|
| 34 | <param name="inputLambda2" value="sequence_from_0_to_0.95_increment_0.05" /> |
---|
| 35 | <param name="inputPI0_method3" value="smoother" /> |
---|
| 36 | <param name="inputFDR_level4" value="0.05" /> |
---|
| 37 | <param name="inputRobust5" value="FALSE" /> |
---|
| 38 | <output name="outputFile1" file="q_values.tabular" /> |
---|
| 39 | <output name="outputFile1" file="p_q_hists_Q_plots.pdf" /> |
---|
| 40 | </test> |
---|
| 41 | </tests> |
---|
| 42 | |
---|
| 43 | <help> |
---|
| 44 | |
---|
| 45 | .. class:: infomark |
---|
| 46 | |
---|
| 47 | **What it does** |
---|
| 48 | |
---|
| 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: |
---|
| 50 | |
---|
| 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. |
---|
| 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. |
---|
| 53 | - The third input is PI method which is either "smoother" or "bootstrap". |
---|
| 54 | - The fourth input is the FDR (false discovery rate) level which is a decimal number between 0.0 and 1.0. |
---|
| 55 | - The fifth input is either TRUE or FALSE for the estimate robustness. |
---|
| 56 | |
---|
| 57 | The program gives two outputs: |
---|
| 58 | |
---|
| 59 | - The first output is a TABULAR format file consisting of three columns: |
---|
| 60 | |
---|
| 61 | - the left column represents the p-values of multiple simultaneous tests, one line for every p-value |
---|
| 62 | - the middle column represents the q-values corresponding to the p-values |
---|
| 63 | - the third column represent the significance values, either 1 for significant or 0 for non-significant |
---|
| 64 | |
---|
| 65 | - The second output is a PDF format file consisting of three pages: |
---|
| 66 | |
---|
| 67 | - the first page represents the p-values histogram |
---|
| 68 | - the second page represents the q-values histogram |
---|
| 69 | - the third page represents the four Q-plots as introduced in the "qvalue" package manual. |
---|
| 70 | |
---|
| 71 | |
---|
| 72 | **Example** |
---|
| 73 | |
---|
| 74 | Let us have the first input file of p-values as follows:: |
---|
| 75 | |
---|
| 76 | 0.140627492 |
---|
| 77 | 0.432249886 |
---|
| 78 | 0.122120877 |
---|
| 79 | 0.142010182 |
---|
| 80 | 0.012909858 |
---|
| 81 | 0.000142807 |
---|
| 82 | 0.039841941 |
---|
| 83 | 0.035173303 |
---|
| 84 | 0.011340057 |
---|
| 85 | 1.01E-05 |
---|
| 86 | 0.212738282 |
---|
| 87 | 0.091256284 |
---|
| 88 | 0.547375415 |
---|
| 89 | 0.189589833 |
---|
| 90 | 6.18E-12 |
---|
| 91 | 0.001235875 |
---|
| 92 | 1.10E-05 |
---|
| 93 | 9.75E-07 |
---|
| 94 | 2.13E-18 |
---|
| 95 | 2.54E-16 |
---|
| 96 | 1.20E-19 |
---|
| 97 | 9.76E-14 |
---|
| 98 | 0.359181534 |
---|
| 99 | 0.03661672 |
---|
| 100 | 0.400459987 |
---|
| 101 | 0.387436466 |
---|
| 102 | 0.342075061 |
---|
| 103 | 0.904129283 |
---|
| 104 | 0.031152635 |
---|
| 105 | |
---|
| 106 | Running the program will give the following output:: |
---|
| 107 | |
---|
| 108 | pi0: 0.140311054 |
---|
| 109 | |
---|
| 110 | FDR level: 0.05 |
---|
| 111 | |
---|
| 112 | p-value q-value significant |
---|
| 113 | 0.1406275 0.02889212 1 |
---|
| 114 | 0.4322499 0.06514199 0 |
---|
| 115 | 0.1221209 0.02760624 1 |
---|
| 116 | 0.1420102 0.02889212 1 |
---|
| 117 | 0.01290986 0.00437754 1 |
---|
| 118 | 0.000142807 6.46E-05 1 |
---|
| 119 | 0.03984194 0.01013235 1 |
---|
| 120 | 0.0351733 0.009932946 1 |
---|
| 121 | 0.01134006 0.004194811 1 |
---|
| 122 | 1.01E-05 5.59E-06 1 |
---|
| 123 | 0.2127383 0.03934711 1 |
---|
| 124 | 0.09125628 0.02184257 1 |
---|
| 125 | 0.5473754 0.07954578 0 |
---|
| 126 | 0.1895898 0.03673547 1 |
---|
| 127 | 6.18E-12 5.03E-12 1 |
---|
| 128 | 0.001235875 0.00050288 1 |
---|
| 129 | 1.10E-05 5.59E-06 1 |
---|
| 130 | 9.75E-07 6.61E-07 1 |
---|
| 131 | 2.13E-18 4.33E-18 1 |
---|
| 132 | 2.54E-16 3.45E-16 1 |
---|
| 133 | 1.20E-19 4.88E-19 1 |
---|
| 134 | 9.76E-14 9.93E-14 1 |
---|
| 135 | 0.3591815 0.06089654 0 |
---|
| 136 | 0.03661672 0.009932946 1 |
---|
| 137 | 0.40046 0.0626723 0 |
---|
| 138 | 0.3874365 0.0626723 0 |
---|
| 139 | 0.3420751 0.06051785 0 |
---|
| 140 | 0.9041293 0.1268593 0 |
---|
| 141 | 0.03115264 0.009750824 1 |
---|
| 142 | |
---|
| 143 | |
---|
| 144 | .. image:: ../static/operation_icons/p_hist.png |
---|
| 145 | |
---|
| 146 | |
---|
| 147 | .. image:: ../static/operation_icons/q_hist.png |
---|
| 148 | |
---|
| 149 | |
---|
| 150 | .. image:: ../static/operation_icons/Q_plots.png |
---|
| 151 | |
---|
| 152 | |
---|
| 153 | </help> |
---|
| 154 | |
---|
| 155 | </tool> |
---|