Annotations of SCOP domain families (fa) by Mammalian Phenotype (MP).
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)
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