Read a Gene Ontology annotation file

Description

Creates a MgsaGoSets using gene ontology annotations provided by a file in GAF 1.0 or 2.0 format.

Usage

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readGAF(filename, evidence=NULL, aspect=c("P", "F", "C"))

Arguments

filename

The name of the Gene Ontology annotation file. It must be in the GAF 1.0 or 2.0 format. It may be gzip-compressed.

evidence

character or NULL. Only annotations with evidence code in evidence are returned. If NULL (default), annotations of all evidence codes are returned.

aspect

character with values in P, C or F. Only annotations of the listed GO namespaces P (biological process), F (molecular function) or C (cellular component) are returned. By default, annotations of the three namespaces are returned.

Details

The function extracts from the annotation file all direct gene annotations and infers from the Gene Ontology all the indirect annotations (due to term relationships). This is done using the package Go.db which provides the ontology as a database and RSQLite for querying the database.

Value

An MgsaGoSets object.

References

The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics, 2000. The GAF file format: http://www.geneontology.org/GO.format.annotation.shtml GO evidence codes: http://www.geneontology.org/GO.evidence.shtml

See Also

MgsaGoSets, mgsa

Examples

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## parsing provided example file (yeast)
gofile = system.file("example_files/gene_association_head.sgd", package="mgsa")
readGAF(gofile)
## only annoations infered from experiment or a direct assay
readGAF(gofile, evidence=c("EXP", "IDA"))

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