Annotations of SCOP domain superfamilies (sf) by UniProtKB UniPathway (UP).

Description

An object of class "Anno" that contains associations between UniProtKB UniPathway terms and SCOP domain superfamilies (sf). This data is prepared based on the dcGO database (see http://supfam.org/SUPERFAMILY/dcGO/).

Usage

SCOP.sf2UP <- dcRDataLoader(RData = "SCOP.sf2UP")

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 SCOP sunid, and "level" for SCOP level, "description" for SCOP description

References

Fang H and Gough J. (2013) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res, 41(Database issue):D536-44.

Examples

# load data SCOP.sf2UP <- dcRDataLoader(RData='SCOP.sf2UP')
'SCOP.sf2UP' (from http://dcgor.r-forge.r-project.org/data/SCOP.sf2UP.RData) has been loaded into the working environment
SCOP.sf2UP
An object of S4 class 'Anno' @annoData: 485 domains, 681 terms @termData (InfoDataFrame) termNames: UPA00026 UPA00485 UPA00942 ... UPA00901 UPA00902 (681 total) tvarLabels: ID Name Namespace Distance @domainData (InfoDataFrame) domainNames: 46548 46565 46589 ... 160088 160355 (485 total) dvarLabels: id level description
# retrieve info on ontology terms termData(SCOP.sf2UP)
An object of S4 class 'InfoDataFrame' rowNames: UPA00026 UPA00485 UPA00942 ... UPA00901 UPA00902 (681 total) colNames: ID Name Namespace Distance
# retrieve info on SCOP domains domainData(SCOP.sf2UP)
An object of S4 class 'InfoDataFrame' rowNames: 46548 46565 46589 ... 160088 160355 (485 total) colNames: id level description
# retrieve the first 5 rows and columns of annotation data x <- annoData(SCOP.sf2UP)[1:5,1:5] x
5 x 5 sparse Matrix of class "dgCMatrix" UPA00461 UPA00194 UPA00196 UPA00462 UPA00463 46548 . . . . . 46565 . . . . . 46589 . . . . . 46626 . . . . . 46689 . . . . .
# convert the above retrieval to the full matrix as.matrix(x)
UPA00461 UPA00194 UPA00196 UPA00462 UPA00463 46548 0 0 0 0 0 46565 0 0 0 0 0 46589 0 0 0 0 0 46626 0 0 0 0 0 46689 0 0 0 0 0

See also

Anno-class