Annotations of Rfam RNA families by Gene Ontology Biological Process (GOBP).

Description

An object of class "Anno" that contains associations between Gene Ontology Biological Process 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

data(Rfam2GOBP)

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.

Examples

# load data data(Rfam2GOBP) Rfam2GOBP
An object of S4 class 'Anno' @annoData: 1377 domains, 76 terms @termData (InfoDataFrame) termNames: GO:0006950 GO:0007275 GO:0009405 ... GO:0000365 GO:0000395 (76 total) tvarLabels: ID Name Namespace Distance @domainData (InfoDataFrame) domainNames: RF00003 RF00004 RF00007 ... RF02272 RF02273 (1377 total) dvarLabels: id level description
# retrieve info on ontology terms termData(Rfam2GOBP)
An object of S4 class 'InfoDataFrame' rowNames: GO:0006950 GO:0007275 GO:0009405 ... GO:0000365 GO:0000395 (76 total) colNames: ID Name Namespace Distance
# retrieve info on Rfam RNAs domainData(Rfam2GOBP)
An object of S4 class 'InfoDataFrame' rowNames: RF00003 RF00004 RF00007 ... RF02272 RF02273 (1377 total) colNames: id level description
# retrieve the first 5 rows and columns of annotation data x <- annoData(Rfam2GOBP)[1:5,1:5] x
5 x 5 sparse Matrix of class "dgCMatrix" GO:0006342 GO:0009098 GO:0009113 GO:0009372 GO:0075139 RF00003 . . . . . RF00004 . . . . . RF00007 . . . . . RF00009 . . . . . RF00010 . . . . .
# convert the above retrieval to the full matrix as.matrix(x)
GO:0006342 GO:0009098 GO:0009113 GO:0009372 GO:0075139 RF00003 0 0 0 0 0 RF00004 0 0 0 0 0 RF00007 0 0 0 0 0 RF00009 0 0 0 0 0 RF00010 0 0 0 0 0

See also

Anno-class