SCOP.fa2GOMF {dcGOR} | R Documentation |
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/).
data(SCOP.fa2GOMF)
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
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.
# 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)