Annotations of Rfam RNA families by Gene Ontology Cellular Component (GOCC).

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Description

An object of class "Anno" that contains associations between Gene Ontology Cellular Component 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.

Usage

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Value

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

References

Gardner et al. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res, 39(Database issue):D141-D145.

See Also

Anno-class

Examples

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# load data
data(Rfam2GOCC)
Rfam2GOCC
# retrieve info on ontology terms
termData(Rfam2GOCC)
# retrieve info on Rfam RNAs
domainData(Rfam2GOCC)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(Rfam2GOCC)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)

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