Annotations of SCOP domain superfamilies (sf) by Disease Ontology (DO).

Description

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

Usage

data(SCOP.sf2DO)

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 data(SCOP.sf2DO) SCOP.sf2DO
An object of S4 class 'Anno' @annoData: 219 domains, 548 terms @termData (InfoDataFrame) termNames: DOID:0014667 DOID:0050117 DOID:0080015 ... DOID:8541 DOID:9849 (548 total) tvarLabels: ID Name Namespace Distance @domainData (InfoDataFrame) domainNames: 46458 46579 46689 ... 161070 161084 (219 total) dvarLabels: id level description
# retrieve info on ontology terms termData(SCOP.sf2DO)
An object of S4 class 'InfoDataFrame' rowNames: DOID:0014667 DOID:0050117 DOID:0080015 ... DOID:8541 DOID:9849 (548 total) colNames: ID Name Namespace Distance
# retrieve info on SCOP domains domainData(SCOP.sf2DO)
An object of S4 class 'InfoDataFrame' rowNames: 46458 46579 46689 ... 161070 161084 (219 total) colNames: id level description
# retrieve the first 5 rows and columns of annotation data x <- annoData(SCOP.sf2DO)[1:5,1:5] x
5 x 5 sparse Matrix of class "dgCMatrix" DOID:0060058 DOID:688 DOID:0000000 DOID:0060061 DOID:0002116 46458 . . . . . 46579 . . . . . 46689 . . . . . 46966 . . . . . 47005 . . . . .
# convert the above retrieval to the full matrix as.matrix(x)
DOID:0060058 DOID:688 DOID:0000000 DOID:0060061 DOID:0002116 46458 0 0 0 0 0 46579 0 0 0 0 0 46689 0 0 0 0 0 46966 0 0 0 0 0 47005 0 0 0 0 0

See also

Anno-class