Pfam2GOMF: Annotations of Pfam domains by Gene Ontology Molecular...

In hfang-bristol/dcGOR: Analysis of Ontologies and Protein Domain Annotations

Annotations of Pfam domains by Gene Ontology Molecular Function (GOMF).

Description

An object of class "Anno" that contains associations between Gene Ontology Molecular Function 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(Pfam2GOMF)

Value

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

• annoData: a sparse matrix of domains X terms

• termData: variables describing ontology terms (i.e. columns in annoData), including: "ID" (i.e. term ID), "Name" (i.e. term Names), "Namespace" (i.e. term Namespace), and "Distance" (i.e. term Distance to the ontology root)

• domainData: variables describing domains (i.e. rows in annoData), including: "id" for Pfam accession ID, and "level" always equals "Pfam", "description" for Pfam description

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(Pfam2GOMF)
Pfam2GOMF
# retrieve info on ontology terms
termData(Pfam2GOMF)
# retrieve info on Pfam domains
domainData(Pfam2GOMF)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(Pfam2GOMF)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)

hfang-bristol/dcGOR documentation built on July 16, 2022, 6:43 p.m.