Map Entrez Gene identifiers to GenBank Accession Numbers

Description

org.Dm.egACCNUM is an R object that contains mappings between Entrez Gene identifiers and GenBank accession numbers.

Details

This object is a simple mapping of Entrez Gene identifiers http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene to all possible GenBank accession numbers.

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

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:
x <- org.Dm.egACCNUM
# Get the entrez gene identifiers that are mapped to an ACCNUM
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the ACCNUM for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}
#For the reverse map ACCNUM2EG:
# Convert to a list
xx <- as.list(org.Dm.egACCNUM2EG)
if(length(xx) > 0){
   # Gets the entrez gene identifiers for the first five Entrez Gene 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)

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.egACCNUM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.Dm.egACCNUM
> ### Title: Map Entrez Gene identifiers to GenBank Accession Numbers
> ### Aliases: org.Dm.egACCNUM org.Dm.egACCNUM2EG
> ### 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:
> x <- org.Dm.egACCNUM
> # Get the entrez gene identifiers that are mapped to an ACCNUM
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+   # Get the ACCNUM for the first five genes
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
[1] "NR_037756" "NR_125093"
> #For the reverse map ACCNUM2EG:
> # Convert to a list
> xx <- as.list(org.Dm.egACCNUM2EG)
> if(length(xx) > 0){
+    # Gets the entrez gene identifiers for the first five Entrez Gene IDs
+    xx[1:5]
+    # Get the first one
+    xx[[1]]
+ }
[1] "30970"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>