An object of class "HIS" that contains annotations and scores between Human Phenotype Phenotypic Abnormality terms and Pfam domains/combinations. This data is prepared based on the dcGO database (see http://supfam.org/SUPERFAMILY/dcGO/).
Feature2HPPA.pfam <- dcRDataLoader(RData = "Feature2HPPA.pfam")
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
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.
# load data Feature2HPPA.pfam <- dcRDataLoader(RData='Feature2HPPA.pfam')'Feature2HPPA.pfam' (from http://dcgor.r-forge.r-project.org/data/Feature2HPPA.pfam.RData) has been loaded into the working environmentnames(Feature2HPPA.pfam) "hscore" "ic" "slim"