R: Map Uniprot accession numbers with Entrez Gene identifiers
hwgcodUNIPROT
R Documentation
Map Uniprot accession numbers with Entrez Gene identifiers
Description
hwgcodUNIPROT is an R object that contains mappings between
the manufacturer identifiers and Uniprot accession numbers.
Details
This object is a simple mapping of manufacturer identifiers to Uniprot
Accessions.
Mappings were based on data provided by NCBI (link above) with an
exception for fly, which required retrieving the data from ensembl
http://www.ensembl.org/biomart/martview/
Examples
x <- hwgcodUNIPROT
# Get the entrez gene IDs that are mapped to an Uniprot ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
# Get the Uniprot IDs for the first five genes
xx[1:5]
# Get the first one
xx[[1]]
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/hwgcodUNIPROT.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hwgcodUNIPROT
> ### Title: Map Uniprot accession numbers with Entrez Gene identifiers
> ### Aliases: hwgcodUNIPROT hwgcodUNIPROT2PROBE
> ### Keywords: datasets
>
> ### ** Examples
>
> x <- hwgcodUNIPROT
> # Get the entrez gene IDs that are mapped to an Uniprot ID
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+ # Get the Uniprot IDs for the first five genes
+ xx[1:5]
+ # Get the first one
+ xx[[1]]
+ }
[1] "P48553"
>
>
>
>
>
> dev.off()
null device
1
>