dcGOR 1.0.5

Annotations and scores between Pfam domains/combinations and Gene Ontology Cellular Component (GOCC).

Description

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

Usage

Feature2GOCC.pfam <- dcRDataLoader(RData = "Feature2GOCC.pfam")

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
Feature2GOCC.pfam <- dcRDataLoader(RData='Feature2GOCC.pfam')


'Feature2GOCC.pfam' (from http://dcgor.r-forge.r-project.org/data/Feature2GOCC.pfam.RData) has been loaded into the working environment

names(Feature2GOCC.pfam)



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