Rfam2GOCC: Annotations of Rfam RNA families by Gene Ontology Cellular...

Description Usage Value References See Also Examples

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)

dcGOR documentation built on May 21, 2017, 3:48 a.m.

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