getOBOCollection {GSEABase} | R Documentation |
getOBOCollection
parses a uri (file or internet location)
encoded following the OBO specification defined by the Gene Onotology
consortium.
getOBOCollection(uri, evidenceCode="ANY", ...)
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. |
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.
Martin Morgan <mtmrogan@fhcrc.org>
## '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)