InterPro2GOBP: Annotations of InterPro domains by Gene Ontology Biological...

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

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

Description

An object of class "Anno" that contains associations between Gene Ontology Biological Process terms and InterPro domains. This data is prepared based on the InterPro database (see http://www.ebi.ac.uk/interpro/) and ftp://[e-mail]/pub/databases/interpro/Current/interpro2go.

Usage

data(InterPro2GOBP)

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 InterPro ID, and "level" always equals "InterPro", "description" for InterPro description

References

Hunter et al. (2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database (Oxford), 2012:bar068.

See Also

Anno-class

Examples

# load data
data(InterPro2GOBP)
InterPro2GOBP
# retrieve info on ontology terms
termData(InterPro2GOBP)
# retrieve info on InterPro domains
domainData(InterPro2GOBP)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(InterPro2GOBP)[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.