Annotations of InterPro domains by Gene Ontology Cellular Component (GOCC).

Description

An object of class "Anno" that contains associations between Gene Ontology Cellular Component terms and InterPro domains. This data is prepared based on the InterPro database (see http://www.ebi.ac.uk/interpro/) and ftp://anonymous@ftp.ebi.ac.uk/pub/databases/interpro/Current/interpro2go.

Usage

data(InterPro2GOCC)

Value

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 InterPro ID, and "level" always equals "InterPro", "description" for InterPro description

References

Hunter et al. (2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database (Oxford), 2012:bar068.

Examples

# load data data(InterPro2GOCC) InterPro2GOCC
An object of S4 class 'Anno' @annoData: 4961 domains, 488 terms @termData (InfoDataFrame) termNames: GO:0005576 GO:0009295 GO:0016020 ... GO:0042729 GO:0044196 (488 total) tvarLabels: ID Name Namespace Distance @domainData (InfoDataFrame) domainNames: IPR000003 IPR000009 IPR000012 ... IPR029781 IPR029782 (4961 total) dvarLabels: id level description
# retrieve info on ontology terms termData(InterPro2GOCC)
An object of S4 class 'InfoDataFrame' rowNames: GO:0005576 GO:0009295 GO:0016020 ... GO:0042729 GO:0044196 (488 total) colNames: ID Name Namespace Distance
# retrieve info on InterPro domains domainData(InterPro2GOCC)
An object of S4 class 'InfoDataFrame' rowNames: IPR000003 IPR000009 IPR000012 ... IPR029781 IPR029782 (4961 total) colNames: id level description
# retrieve the first 5 rows and columns of annotation data x <- annoData(InterPro2GOCC)[1:5,1:5] x
5 x 5 sparse Matrix of class "dgCMatrix" GO:0000220 GO:0000221 GO:0045281 GO:0000228 GO:0072546 IPR000003 . . . . . IPR000009 . . . . . IPR000012 . . . . . IPR000013 . . . . . IPR000015 . . . . .
# convert the above retrieval to the full matrix as.matrix(x)
GO:0000220 GO:0000221 GO:0045281 GO:0000228 GO:0072546 IPR000003 0 0 0 0 0 IPR000009 0 0 0 0 0 IPR000012 0 0 0 0 0 IPR000013 0 0 0 0 0 IPR000015 0 0 0 0 0

See also

Anno-class