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Up: Component summary
Component
GOFilterFilters gene lists based on Gene Ontology annotations. Only genes that are annotated with given GO terms are selected for output. This component takes the parent-child relationships of GO into account: a gene is annotated with a given GO term if it has annotation entries either for the exact GO term or some child term.
You may use GOSearch if you are interested in the actual mapping between the query terms and the matches or if you want to avoid R and Bioconductor.
| Version | 1.2 |
|---|---|
| Bundle | microarray |
| Categories | Filter GO |
| Authors | Kristian Ovaska (kristian.ovaska@helsinki.fi), Marko Laakso (Marko.Laakso@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | R ; AnnotationDbi (R-bioconductor) ; GO.db (R-bioconductor) |
| Source files | component.xml GOFilter.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| bioAnnotation | AnnotationTable | Mandatory | Annotations that are used as the basis for filtering. |
| in | SetList | Optional | List of genes of interest. Genes of the annotation file are used if this input is missing. |
Outputs| Name | Type | Description |
|---|---|---|
| out | SetList | Filtered gene sets. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| geneColumn | string | "" | Name of the gene ID column or an empty string referring to the first ID column of the table. |
| goColumn | string | "GO" | Name of the GO annotation column |
| numMatches | int | 1 | Required number of matching terms for the gene to be selected for output. This must be between 1 and n, where n is the number of terms. If numMatches is 1, a gene must be annotated with at least one GO term mentioned in 'terms'. If numMatches in n, a gene must be annotated with all GO terms. |
| setID | string | "%s_GOMatch" | Name of the result sets. The pattern %s is expanded to the name of each set in question. |
| terms | string | (no default) | Comma-separated list of GO terms that are used for filtering. |
Test cases| Test case | Parameters▼ | IN bioAnnotation |
IN in |
OUT out |
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|---|---|---|---|---|---|---|
| case1_num_matches_1 | properties | bioAnnotation | in | out | ||
|
terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089 |
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| case2_num_matches_2 | properties | bioAnnotation | in | out | ||
|
terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089, |
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| case3_num_matches_3 | properties | bioAnnotation | in | out | ||
|
terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089, |
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| case4_num_matches_4 | properties | bioAnnotation | in | out | ||
|
terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089, |
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| case5_no_groups | properties | bioAnnotation | (missing) | out | ||
|
terms=GO:0050896,GO:0032501,GO:0016020,GO:0005488,GO:0060089, |
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