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GOProbabilityTable

Creates custom a priori probability tables for GO similarity and enrichment analysis. The tables are used by the R package csbl.go, which is used by e.g., the GOClustering component.

The csbl.go R package is available at http://csbi.ltdk.helsinki.fi/csbl.go/.

Version 1.0
Bundle microarray
Categories Annotation GO
Authors Kristian Ovaska (kristian.ovaska@helsinki.fi)
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Requires csbl.go (R-package)
Source files component.xml GOProbabilityTable.r
Usage Example with default values

Inputs

Name Type Mandatory Description
goAnnotation CSV Mandatory GO annotations for a gene set. Often, the gene set is the whole genome or the genes from a microarray. The first column must be gene IDs and GO annotations must be present in some other column. It does not matter which column contains GO annotations since each line is scanned with a regular expression that locates all GO terms.

Outputs

Name Type Description
similarityTable CSV GO probability table for similarity computation
enrichmentTable CSV GO probability table for enrichment analysis

Test cases

Test case Parameters IN
goAnnotation
OUT
similarityTable
OUT
enrichmentTable
case1 (missing) goAnnotation (missing) (missing)
case2_empty (missing) goAnnotation (missing) (missing)

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