root/galaxy-central/tools/regVariation/compute_q_values.xml

リビジョン 2, 4.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
49This 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
57The 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
74Let 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
106Running 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>
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