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

リビジョン 2, 2.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="rcve1" name="Compute RCVE" version="1.0.0">
2  <description> </description>
3  <command interpreter="python">
4    rcve.py
5      $input1
6      $response_col
7      $predictor_cols
8      $out_file1
9      1>/dev/null
10  </command>
11  <inputs>
12    <param format="tabular" name="input1" type="data" label="Select data" help="Query missing? See TIP below."/>
13    <param name="response_col" label="Response column (Y)" type="data_column" data_ref="input1" />
14    <param name="predictor_cols" label="Predictor columns (X)" type="data_column" data_ref="input1" multiple="true">
15        <validator type="no_options" message="Please select at least one column."/>
16    </param>
17  </inputs>
18  <outputs>
19    <data format="input" name="out_file1" metadata_source="input1" />
20  </outputs>
21  <requirements>
22    <requirement type="python-module">rpy</requirement>
23  </requirements>
24  <tests>
25    <!-- Test data with vlid values -->
26        <test>
27      <param name="input1" value="reg_inp.tab"/>
28      <param name="response_col" value="1"/>
29      <param name="predictor_cols" value="2,3,4"/>
30      <output name="out_file1" file="rcve_out.dat"/>
31    </test>
32   
33  </tests>
34  <help>
35
36.. class:: infomark
37
38**TIP:** If your data is not TAB delimited, use *Edit Queries-&gt;Convert characters*
39
40-----
41
42.. class:: infomark
43
44**What it does**
45
46This tool computes the RCVE (Relative Contribution to Variance) for all possible variable subsets using the following formula:
47
48**RCVE(i) = [R-sq (full: 1,2,..,i..,p-1) - R-sq(without i: 1,2,...,p-1)] / R-sq (full: 1,2,..,i..,p-1)**,
49which denotes the case where the 'i'th predictor is dropped.
50
51
52In general,
53**RCVE(X+) = [R-sq (full: {X,X+}) - R-sq(reduced: {X})] / R-sq (full: {X,X+})**,
54where,
55
56- {X,X+} denotes the set of all predictors,
57- X+ is the set of predictors for which we compute RCVE (and therefore drop from the full model to obtain a reduced one),
58- {X} is the set of the predictors that are left in the reduced model after excluding {X+}
59
60
61The 4 columns in the output are described below:
62
63- Column 1 (Model): denotes the variables present in the model ({X})
64- Column 2 (R-sq): denotes the R-squared value corresponding to the model in Column 1
65- Column 3 (RCVE_Terms): denotes the variable/s for which RCVE is computed ({X+}). These are the variables that are absent in the reduced model in Column 1. A '-' in this column indicates that the model in Column 1 is the Full model.
66- Column 4 (RCVE): denotes the RCVE value corresponding to the variable/s in Column 3. A '-' in this column indicates that the model in Column 1 is the Full model.
67 
68 
69  </help>
70</tool>
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