getSymbols: Convert entrez gene IDs to gene symbols

In GeneAnswers: Integrated Interpretation of Genes

Description

function to convert given entrez gene IDs to gene symbols.

Usage

getSymbols(geneIDs, data, strict = FALSE, missing=c('name', 'keep', 'remove'))

Arguments

geneIDs	an Entrez gene IDs vector
data	annotation library
strict	logic value to stop conversion if NA is introduced.
missing	type of handling NA mapping.

Value

return a gene symbols vector of given gene IDs. There are three types of parameters for variable 'missing'. 'name' means the NA mapping values are replaced by their names. 'keep' means all of NA values are kept. 'remove' means all of NA values are removed.

Author(s)

Gang Feng, Pan Du and Simon Lin

References

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

Examples

require('org.Mm.eg.db')
getSymbols(c('11651', '11836'), 'org.Mm.eg.db')

Example output

Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: RCurl
Loading required package: bitops
Loading required package: annotate
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:igraph':

    normalize, path, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

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 object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: RSQLite
Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':

    select

Loading required package: Heatplus
Loading required package: RColorBrewer
Warning messages:
1: replacing previous import 'stats::decompose' by 'igraph::decompose' when loading 'GeneAnswers' 
2: replacing previous import 'stats::spectrum' by 'igraph::spectrum' when loading 'GeneAnswers' 
Loading required package: org.Mm.eg.db

 11651  11836 
"Akt1" "Araf" 

GeneAnswers documentation built on Nov. 8, 2020, 4:53 p.m.