An object of class "Anno" that contains associations between Mammalian Phenotype terms and SCOP domain families (fa). This data is prepared based on the dcGO database (see http://supfam.org/SUPERFAMILY/dcGO/).
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
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.
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# load data data(SCOP.fa2MP) SCOP.fa2MP # retrieve info on ontology terms termData(SCOP.fa2MP) # retrieve info on SCOP domains domainData(SCOP.fa2MP) # retrieve the first 5 rows and columns of annotation data x <- annoData(SCOP.fa2MP)[1:5,1:5] x # convert the above retrieval to the full matrix as.matrix(x)