Mercurial > repos > miller-lab > genome_diversity

annotate rank_terms.xml @ 30:4188853b940b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to Miller Lab devshed revision eb4e61d024db
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 26 Jul 2013 12:51:13 -0400
parents 8997f2ca8c7a
children a631c2f6d913
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
1 <tool id="gd_rank_terms" name="Rank Terms" version="1.1.0">
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
2 <description>: Assess the enrichment/depletion of a gene set for GO terms</description>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
3
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
4 <command interpreter="python">
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
5 #set $t_col1_0 = int(str($t_col1)) - 1
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
6 #set $t_col2_0 = int(str($t_col2)) - 1
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
7 #set $g_col2_0 = int(str($g_col2)) - 1
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
8 rank_terms.py --input "$input1" --columnENSEMBLT $t_col1_0 --inExtnddfile "$input2" --columnENSEMBLTExtndd $t_col2_0 --columnGOExtndd $g_col2_0 --statsTest "$stat" --output "$output"
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
9 </command>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
10
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
11 <inputs>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
12 <param name="input1" type="data" format="tabular" label="Query dataset" />
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
13 <param name="t_col1" type="data_column" data_ref="input1" label="Column with ENSEMBL transcript codes" />
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
14 <param name="input2" type="data" format="tabular" label="Background dataset" />
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
15 <param name="t_col2" type="data_column" data_ref="input2" label="Column with ENSEMBL transcript codes" />
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
16 <param name="g_col2" type="data_column" data_ref="input2" label="Column with GO terms" />
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
17 <param name="stat" type="select" label="Statistic for determining enrichment/depletion">
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
18 <option value="fisher" selected="true">two-tailed Fisher's exact test</option>
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
19 <option value="hypergeometric">hypergeometric test</option>
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
20 <option value="binomial">binomial probability</option>
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
21 </param>
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
22 </inputs>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
23
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
24 <outputs>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
25 <data name="output" format="tabular" />
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
26 </outputs>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
27
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
28 <help>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
29
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
30 **Dataset formats**
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
31
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
32 All of the input and output datasets are in tabular_ format.
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
33 The query dataset has a column containing ENSEMBL transcript codes for
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
34 the gene set of interest, while the background dataset has one column
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
35 with ENSEMBL transcript codes and another with GO terms, for some
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
36 larger universe of genes.
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
37 The output dataset is described below.
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
38 (`Dataset missing?`_)
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
39
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
40 .. _tabular: ./static/formatHelp.html#tab
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
41 .. _Dataset missing?: ./static/formatHelp.html
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
42
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
43 -----
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
44
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
45 **What it does**
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
46
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
47 Given a query set of genes from a larger background dataset, this tool
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
48 evaluates the over- or under-representation of Gene Ontology terms in the
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
49 query set, using the specified statistical test.
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
50
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
51 The output contains a row for each GO term, with the following columns:
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
52
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
53 1. count: the number of genes in the query set that are in this GO category
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
54 2. representation: the percentage of this category's genes (from the background dataset) that appear in the query set
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
55 3. ranking of this term, based on its representation ("1" is highest)
27
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
56 4. probability of depletion of this GO category in the query dataset
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
57 5. probability of enrichment of this GO category in the query dataset
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents: 22
diff changeset
58 6. GO term
22
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
59
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
60 </help>
95a05c1ef5d5 update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
61 </tool>