Map Ensembl gene accession numbers with Entrez Gene identifiers

Description

illuminaMousev1p1ENSEMBL is an R object that contains mappings between manufacturer identifiers and Ensembl gene accession numbers.

Details

This object is a simple mapping of manufacturer identifiers to Ensembl gene Accession Numbers.

Mappings were based on data provided by BOTH of these sources: http://www.ensembl.org/biomart/martview/ ftp://ftp.ncbi.nlm.nih.gov/gene/DATA

For most species, this mapping is a combination of manufacturer to ensembl IDs from BOTH NCBI and ensembl. Users who wish to only use mappings from NCBI are encouraged to see the ncbi2ensembl table in the appropriate organism package. Users who wish to only use mappings from ensembl are encouraged to see the ensembl2ncbi table which is also found in the appropriate organism packages. These mappings are based upon the ensembl table which is contains data from BOTH of these sources in an effort to maximize the chances that you will find a match.

For worms and flies however, this mapping is based only on sources from ensembl, as these organisms do not have ensembl to entrez gene mapping data at NCBI.

Examples

    x <- illuminaMousev1p1ENSEMBL
    # Get the entrez gene IDs that are mapped to an Ensembl ID
    mapped_genes <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_genes])
    if(length(xx) > 0) {
      # Get the Ensembl gene IDs for the first five genes
      xx[1:5]
      # Get the first one
      xx[[1]]
    }
    #For the reverse map ENSEMBL2PROBE:
    # Convert to a list
    xx <- as.list(illuminaMousev1p1ENSEMBL2PROBE)
    if(length(xx) > 0){
       # Gets the entrez gene IDs for the first five Ensembl IDs
       xx[1:5]
       # Get the first one
       xx[[1]]
    }

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)

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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
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Type 'q()' to quit R.

> library(illuminaMousev1p1.db)
Loading required package: AnnotationDbi
Loading required package: stats4
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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: org.Mm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaMousev1p1.db/illuminaMousev1p1ENSEMBL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev1p1ENSEMBL
> ### Title: Map Ensembl gene accession numbers with Entrez Gene identifiers
> ### Aliases: illuminaMousev1p1ENSEMBL illuminaMousev1p1ENSEMBL2PROBE
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     x <- illuminaMousev1p1ENSEMBL
>     # Get the entrez gene IDs that are mapped to an Ensembl ID
>     mapped_genes <- mappedkeys(x)
>     # Convert to a list
>     xx <- as.list(x[mapped_genes])
>     if(length(xx) > 0) {
+       # Get the Ensembl gene IDs for the first five genes
+       xx[1:5]
+       # Get the first one
+       xx[[1]]
+     }
[1] "ENSMUSG00000037418"
>     #For the reverse map ENSEMBL2PROBE:
>     # Convert to a list
>     xx <- as.list(illuminaMousev1p1ENSEMBL2PROBE)
>     if(length(xx) > 0){
+        # Gets the entrez gene IDs for the first five Ensembl IDs
+        xx[1:5]
+        # Get the first one
+        xx[[1]]
+     }
[1] "ILMN_2688905"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>