Up: Component summary
Up: Component summary
Component
GOProbabilityTableCreates 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) |
| Issue tracker | View/Report issues |
| 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) |