Rfam2GOMF {dcGOR} | R Documentation |
An object of class "Anno" that contains associations between Gene Ontology Molecular Function terms and Rfam RNA families. This data is prepared based on the Rfam database (see http://rfam.xfam.org) and http://geneontology.org/external2go/rfam2go.
data(Rfam2GOMF)
an object of class Anno
. It has slots for "annoData",
"termData" and "domainData":
annoData
: a sparse matrix of RNAs 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 RNAs (i.e. rows in
annoData), including: "id" for Rfam accession ID, and "level" always
equals "Rfam", "description" for Rfam description
Gardner et al. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res, 39(Database issue):D141-D145.
# load data
data(Rfam2GOMF)
Rfam2GOMF
# retrieve info on ontology terms
termData(Rfam2GOMF)
# retrieve info on Rfam RNAs
domainData(Rfam2GOMF)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(Rfam2GOMF)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)