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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PSICQUIC)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: biomaRt
Loading required package: httr
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PSICQUIC/IDMapper-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IDMapper-class
> ### Title: IDMapper
> ### Aliases: class:IDMapper IDMapper-class IDMapper addGeneInfo
> ###   addGeneInfo,IDMapper-method S4method{addGeneInfo}{IDMapper}
> ###   addStandardNames addStandardNames,IDMapper-method
> ###   S4method{addStandardNames}{IDMapper}
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>    mapper <- IDMapper("9606")
checking for biomart access...
   does 'http://www.ensembl.org' respond?
   creating ensembl mart
   hsapiens_gene_ensembl dataset provided?
connecting to biomart...
>    tbl <- data.frame(A="entrez gene/locuslink:238|BIOGRID:106739",
+                      B="entrez gene/locuslink:3718|BIOGRID:109921",
+                      stringsAsFactors=FALSE)
>    tbl.withGeneInfo <- addGeneInfo(mapper, tbl)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>