SCOP.fa2GOMF {dcGOR}

R Documentation

Annotations of SCOP domain families (fa) by Gene Ontology Molecular Function (GOMF).

Description

An object of class "Anno" that contains associations between Gene Ontology Molecular Function terms and SCOP domain families (fa). This data is prepared based on the dcGO database (see http://supfam.org/SUPERFAMILY/dcGO/).

Usage

data(SCOP.fa2GOMF)

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 SCOP sunid, and "level" for SCOP level, "description" for SCOP description

References

Fang H and Gough J. (2013) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res, 41(Database issue):D536-44.

See Also

Anno-class

Examples

# load data
data(SCOP.fa2GOMF)
SCOP.fa2GOMF
# retrieve info on ontology terms
termData(SCOP.fa2GOMF)
# retrieve info on SCOP domains
domainData(SCOP.fa2GOMF)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.fa2GOMF)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)

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