Map between Common Gene Symbol Identifiers and Entrez Gene

Description

org.Dm.egALIAS is an R object that provides mappings between common gene symbol identifiers and entrez gene identifiers.

Details

Each gene symbol maps to a named vector containing the corresponding entrez gene identifier. The name of the vector corresponds to the gene symbol. Since gene symbols are sometimes redundantly assigned in the literature, users are cautioned that this map may produce multiple matching results for a single gene symbol. Users should map back from the entrez gene IDs produced to determine which result is the one they want when this happens.

Because of this problem with redundant assigment of gene symbols, is it never advisable to use gene symbols as primary identifiers.

This mapping includes ALL gene symbols including those which are already listed in the SYMBOL map. The SYMBOL map is meant to only list official gene symbols, while the ALIAS maps are meant to store all used symbols.

Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA With a date stamp from the source of: 2016-Mar14

References

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene

See Also

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
# Convert the object to a list
xx <- as.list(org.Dm.egALIAS2EG)
# Remove pathway identifiers that do not map to any entrez gene id
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
    # The entrez gene identifiers for the first two elements of XX
    xx[1:2]
    # 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)

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(org.Dm.eg.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


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/org.Dm.eg.db/org.Dm.egALIAS2EG.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Dm.egALIAS2EG
> ### Title: Map between Common Gene Symbol Identifiers and Entrez Gene
> ### Aliases: org.Dm.egALIAS2EG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
> 
> ## Bimap interface:
> # Convert the object to a list
> xx <- as.list(org.Dm.egALIAS2EG)
> # Remove pathway identifiers that do not map to any entrez gene id
> xx <- xx[!is.na(xx)]
> if(length(xx) > 0){
+     # The entrez gene identifiers for the first two elements of XX
+     xx[1:2]
+     # Get the first one
+     xx[[1]]
+ }
[1] "30970"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>