Feature2HPPA.sf: Annotations and scores between SCOP domains/combinations (at...

In hfang-bristol/dcGOR: Analysis of Ontologies and Protein Domain Annotations

Annotations and scores between SCOP domains/combinations (at the superfamily level; sf) and Human Phenotype Phenotypic Abnormality (HPPA).

Description

An object of class "HIS" that contains annotations and scores between Human Phenotype Phenotypic Abnormality terms and SCOP domains/combinations (at the superfamily level; sf). This data is prepared based on the dcGO database (see http://supfam.org/SUPERFAMILY/dcGO/).

Usage

Feature2HPPA.sf <- dcRDataLoader(RData='Feature2HPPA.sf')

Value

an object of class HIS. It has three components for "hscore", "ic" and "slim":

• hscore: a list of domain-related features, each with a term-named vector containing hypergeometric score (hscore)

• ic: a term-named vector containing information content (IC). Terms are ordered first by IC and then by longest-path level, making sure that for terms with the same IC, parental terms always come first

• slim: a list of four slims, each with a term-named vector containing information content (IC). Slim '1' for very general terms, '2' for general terms, '3' for specific terms, '4' for very specific terms

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.
Fang H and Gough J. (2013) A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics, 14(Suppl 3):S9.

Examples

# load data
Feature2HPPA.sf <- dcRDataLoader(RData='Feature2HPPA.sf')
names(Feature2HPPA.sf)

hfang-bristol/dcGOR documentation built on July 16, 2022, 6:43 p.m.