Annotations of SCOP domain families (fa) by Enzyme Commission (EC).

Description

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

Usage

SCOP.fa2EC <- dcRDataLoader(RData = "SCOP.fa2EC")

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.fa2EC <- dcRDataLoader(RData='SCOP.fa2EC')
'SCOP.fa2EC' (from http://dcgor.r-forge.r-project.org/data/SCOP.fa2EC.RData) has been loaded into the working environment
SCOP.fa2EC
An object of S4 class 'Anno' @annoData: 1406 domains, 1698 terms @termData (InfoDataFrame) termNames: 1 2 3 ... 6.5.1.3 6.5.1.4 (1698 total) tvarLabels: ID Name Namespace Distance @domainData (InfoDataFrame) domainNames: 46463 46549 46553 ... 161204 161211 (1406 total) dvarLabels: id level description
# retrieve info on ontology terms termData(SCOP.fa2EC)
An object of S4 class 'InfoDataFrame' rowNames: 1 2 3 ... 6.5.1.3 6.5.1.4 (1698 total) colNames: ID Name Namespace Distance
# retrieve info on SCOP domains domainData(SCOP.fa2EC)
An object of S4 class 'InfoDataFrame' rowNames: 46463 46549 46553 ... 161204 161211 (1406 total) colNames: id level description
# retrieve the first 5 rows and columns of annotation data x <- annoData(SCOP.fa2EC)[1:5,1:5] x
5 x 5 sparse Matrix of class "dgCMatrix" 1 1.1.1.102 1.1.1.37 1.3.1 1.3.1.10 46463 1 . . . . 46549 1 . . . . 46553 1 . . 1 . 46586 . . . . . 46590 . . . . .
# convert the above retrieval to the full matrix as.matrix(x)
1 1.1.1.102 1.1.1.37 1.3.1 1.3.1.10 46463 1 0 0 0 0 46549 1 0 0 0 0 46553 1 0 0 1 0 46586 0 0 0 0 0 46590 0 0 0 0 0

See also

Anno-class