limma (version 3.28.6)

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 are "Dm", "Hs", "Mm" or "Rn".

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. Possible species are "Dm" for fly, "Hs" for human, "Mm" for mouse and "Rn" for rat. The appropriate Bioconductor organism package is assumed to be installed. 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.

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)