limma (version 3.28.14)

alias2Symbol: Convert Gene Aliases to Official Gene Symbols

Description

Maps gene alias names to official gene symbols.

Usage

alias2Symbol(alias, species = "Hs", expand.symbols = FALSE) alias2SymbolTable(alias, species = "Hs")

Arguments

alias
character vector of gene aliases
species
character string specifying the species. Possible values include "Hs" (human), "Mm" (mouse), "Rn" (rat), "Dm" (fly) or "Pt" (chimpanzee), but other values are possible if the corresponding organism package is available.
expand.symbols
logical. This affects those elements of alias that are the official gene symbol for one gene and also an alias for another gene. If FALSE, then these elements will just return themselves. If TRUE, then all the genes for which they are aliases will be returned.

Value

Character vector of gene symbols.alias2SymbolTable returns a vector of the same length and order as alias, including NA values where no gene symbol was found. alias2Symbol returns an unordered vector that may be longer or shorter than alias.

Details

Aliases are mapped via NCBI Entrez Gene identity numbers using Bioconductor organism packages.

alias2Symbol maps a set of aliases to a set of symbols, without necessarily preserving order. The output vector may be longer or shorter than the original vector, because some aliases might not be found and some aliases may map to more than one symbol. alias2SymbolTable maps each alias to a gene symbol and returns a table with one row for each alias. If an alias maps to more than one symbol, then the first one found is returned.

species can be any character string XX for which an organism package org.XX.eg.db exists and is installed. The only requirement of the organism package is that it contains objects org.XX.egALIAS2EG and org.XX.egSYMBOL linking the aliases and symbols to Entrez Gene Ids. At the time of writing (June 2016), the following organism packages are available from Bioconductor:

Package
Species
org.Ag.eg.db Anopheles
org.Bt.eg.db
Bovine
org.Ce.eg.db Worm
org.Cf.eg.db
Canine
org.Dm.eg.db Fly
org.Dr.eg.db
Zebrafish
org.EcK12.eg.db E coli strain K12
org.EcSakai.eg.db
E coli strain Sakai
org.Gg.eg.db Chicken
org.Hs.eg.db
Human
org.Mm.eg.db Mouse
org.Mmu.eg.db
Rhesus
org.Pt.eg.db Chimp
org.Rn.eg.db
Rat
org.Ss.eg.db Pig

See Also

This function is often used to assist gene set testing, see 10.GeneSetTests.

Examples

alias2Symbol(c("PUMA","NOXA","BIM"), species="Hs")
alias2Symbol("RS1", expand=TRUE)