IDMapper-class: IDMapper

In paul-shannon/PSICQUIC: Proteomics Standard Initiative Common QUery InterfaCe

IDMapper

Description

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 mapping. The addGeneInfo method adds four columns to the data.frame it is passed: gene symbol and geneID for both interacting proteins.

Usage

IDMapper(species)
## S4 method for signature 'IDMapper'
addGeneInfo(object, tbl)

Arguments

species	a character string, as specified by the NCBI. Only "9606" (Homo sapiens) is currently supported.
object	a PSICQUIC object.
tbl	A data.frame such as one returned by the interactions method. Columns named A and B are required, and are presumed to contain PSICQUIC provider identifers in a few formats. Most, but not all identifiers returned by all PSICQUIC providers are recognized.

Value

A copy of the data.frame passed in, with 4 columns added: A.name, B.name, A.id, B.id.

Constructor

IDMapper(species): only human ("9606") is currently supported.

Methods

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

Author(s)

Paul Shannon

See Also

providers, interactions, rawQuery, addGeneInfo, IDMapper, interactionTypes, detectionMethods, speciesIDs

Examples

   mapper <- IDMapper("9606")
   tbl <- data.frame(A="entrez gene/locuslink:238|BIOGRID:106739",
                     B="entrez gene/locuslink:3718|BIOGRID:109921",
                     stringsAsFactors=FALSE)
   tbl.withGeneInfo <- addGeneInfo(mapper, tbl)

paul-shannon/PSICQUIC documentation built on Oct. 19, 2024, 3:26 a.m.