dcGOR 1.0.5

Annotations and scores between InterPro domains and Gene Ontology Molecular Function (GOMF).

Description

An object of class "HIS" that contains annotations and scores between Gene Ontology Molecular Function terms and InterPro domains. This data is prepared based on the dcGO database (see http://supfam.org/SUPERFAMILY/dcGO/).

Usage

Feature2GOMF.interpro <- dcRDataLoader(RData = "Feature2GOMF.interpro")

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
Feature2GOMF.interpro <- dcRDataLoader(RData='Feature2GOMF.interpro')


'Feature2GOMF.interpro' (from http://dcgor.r-forge.r-project.org/data/Feature2GOMF.interpro.RData) has been loaded into the working environment

names(Feature2GOMF.interpro)



[1] "hscore" "ic"     "slim"