PSICQUIC-compliant services typically return verbose protein identifiers
for the interactions they report. However, we often wish to know the
entrez geneID or HUGO symbol of the gene associated with the
interacting protein. The IDMapper class, using biomaRt, provides that
addGeneInfo method adds four columns to the
data.frame it is passed: gene symbol and geneID for both interacting proteins.
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IDMapper(species) ## S4 method for signature 'IDMapper' addGeneInfo(object, tbl)
A copy of the data.frame passed in, with 4 columns added: A.name, B.name, A.id, B.id.
IDMapper(species): only human ("9606") is currently supported.
addGeneInfo(object,tbl): add geneID and symbol for the A and B columns in the data.frame "tbl", which is expected to be a result returned by the interactions method.
addStandardNames(object,tbl): A.name, A.id, B.name, B.id
providers, interactions, rawQuery, addGeneInfo, IDMapper, interactionTypes, detectionMethods, speciesIDs
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