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author devteam
date Tue, 20 Aug 2013 09:34:16 -0400
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1 <tool id="compute_q_values" name="Compute q-values" version="1.0.1">
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_path}/operation_icons/p_hist.png
145
146
147 .. image:: ${static_path}/operation_icons/q_hist.png
148
149
150 .. image:: ${static_path}/operation_icons/Q_plots.png
151
152
153 </help>
154
155 </tool>