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author devteam
date Tue, 01 Apr 2014 10:53:54 -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 <requirements>
4 <requirement type="package" version="2.11.0">R</requirement>
5 <requirement type="package" version="1.34.0">bioc_qvalue</requirement>
6 </requirements>
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
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"/>
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
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"/>
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
147 .. image:: ${static_path}/operation_icons/p_hist.png
148
149
150 .. image:: ${static_path}/operation_icons/q_hist.png
151
152
153 .. image:: ${static_path}/operation_icons/Q_plots.png
154
155
156 </help>
157
158 </tool>