Annotations of SCOP domain superfamilies (sf) by Human Phenotype Phenotypic Abnormality (HPPA).

Description

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

Usage

data(SCOP.sf2HPPA)

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.sf2HPPA) SCOP.sf2HPPA
An object of S4 class 'Anno' @annoData: 166 domains, 844 terms @termData (InfoDataFrame) termNames: HP:0000119 HP:0000152 HP:0000478 ... HP:0010194 HP:0001274 (844 total) tvarLabels: ID Name Namespace Distance @domainData (InfoDataFrame) domainNames: 46458 46565 46579 ... 160481 161070 (166 total) dvarLabels: id level description
# retrieve info on ontology terms termData(SCOP.sf2HPPA)
An object of S4 class 'InfoDataFrame' rowNames: HP:0000119 HP:0000152 HP:0000478 ... HP:0010194 HP:0001274 (844 total) colNames: ID Name Namespace Distance
# retrieve info on SCOP domains domainData(SCOP.sf2HPPA)
An object of S4 class 'InfoDataFrame' rowNames: 46458 46565 46579 ... 160481 161070 (166 total) colNames: id level description
# retrieve the first 5 rows and columns of annotation data x <- annoData(SCOP.sf2HPPA)[1:5,1:5] x
5 x 5 sparse Matrix of class "dgCMatrix" HP:0000119 HP:0010978 HP:0002843 HP:0001454 HP:0002846 46458 . . . . . 46565 . . . . . 46579 . . . . . 46689 . . . . . 46774 . . . . .
# convert the above retrieval to the full matrix as.matrix(x)
HP:0000119 HP:0010978 HP:0002843 HP:0001454 HP:0002846 46458 0 0 0 0 0 46565 0 0 0 0 0 46579 0 0 0 0 0 46689 0 0 0 0 0 46774 0 0 0 0 0

See also

Anno-class