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 <- hwgcodENSEMBL
# 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(hwgcodENSEMBL2PROBE)
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)
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(hwgcod.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.Hs.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/hwgcod.db/hwgcodENSEMBL.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hwgcodENSEMBL
> ### Title: Map Ensembl gene accession numbers with Entrez Gene identifiers
> ### Aliases: hwgcodENSEMBL hwgcodENSEMBL2PROBE
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- hwgcodENSEMBL
> # 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] "ENSG00000160218"
> #For the reverse map ENSEMBL2PROBE:
> # Convert to a list
> xx <- as.list(hwgcodENSEMBL2PROBE)
> 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] "GE80317"
>
>
>
>
>
> dev.off()
null device
1
>