getOBOCollection {GSEABase} | R Documentation

## Read OBO-specified Gene Ontology Collections

### Description

`getOBOCollection` parses a uri (file or internet location) encoded following the OBO specification defined by the Gene Onotology consortium.

### Usage

    getOBOCollection(uri, evidenceCode="ANY", ...)

### Arguments

`uri` | A file name or URL containing gene sets encoded following the OBO specification.
`evidenceCode` | A character vector of evidence codes.
`...` | Further arguments passed to the `OBOCollection` constructor.

### Value

`getOBOCollection` returns an `OBOCollection` of gene sets. The gene set is constructed by parsing the file for `id` tags in `TERM` stanzas. The parser does not currently support all features of OBO, e.g., the ability to import additional files.

### Author(s)

Martin Morgan <mtmrogan@fhcrc.org>

### References

http://www.geneontology.org

### See Also

`OBOCollection`, `OBOCollection`

### Examples

    ## 'fl' could also be a URI
    fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
    getOBOCollection(fl) # GeneSetCollection of 2 sets

    ## Not run:
    ## Download from the internet
    fl <- "http://www.geneontology.org/GO_slims/goslim_plant.obo"
    getOBOCollection(fl, evidenceCode="TAS")

    ## End(Not run)

[Package GSEABase version 1.54.0 Index]