Annotations of SCOP domain families (fa) by Human Phenotype Mode of Inheritance (HPMI).

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Description

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

Usage

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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.

See Also

Anno-class

Examples

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# load data
data(SCOP.fa2HPMI)
SCOP.fa2HPMI
# retrieve info on ontology terms
termData(SCOP.fa2HPMI)
# retrieve info on SCOP domains
domainData(SCOP.fa2HPMI)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.fa2HPMI)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)

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