Pfam2GOBP {dcGOR}R Documentation

Annotations of Pfam domains by Gene Ontology Biological Process (GOBP).

Description

An object of class "Anno" that contains associations between Gene Ontology Biological Process terms and Pfam domains. This data is prepared based on the Pfam database (see http://pfam.xfam.org) and ftp://ftp.geneontology.org/pub/go/external2go/pfam2go.

Usage

data(Pfam2GOBP)

Value

an object of class Anno. It has slots for "annoData", "termData" and "domainData":

References

Finn et al. (2014) The Pfam protein families database. Nucleic Acids Res, 42(Database issue):D222-D230.

See Also

Anno-class

Examples

# load data
data(Pfam2GOBP)
Pfam2GOBP
# retrieve info on ontology terms
termData(Pfam2GOBP)
# retrieve info on Pfam domains
domainData(Pfam2GOBP)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(Pfam2GOBP)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)

[Package dcGOR version 1.0.6 Index]