alias2Symbol: Convert Gene Alias to Official Gene Symbols

In richierocks/limma2: Linear Models for Microarray Data

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, should those elements of alias which are already official symbols be expanded if they are aliases for other symbols.

Details

Aliases are mapped via NCBI Entrez Gene identity numbers using Bioconductor organism packages. Species are "Dm" for fly, "Hs" for human, "Mm" for mouse and "Rn" for rat. The user needs to have the appropriate Bioconductor organism package 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 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 which may be longer or shorter than alias.

Author(s)

Gordon Smyth and Yifang Hu

See Also

This function is often used to assist gene set testing, see 08.Tests.

Examples

if(require("org.Hs.eg.db")) alias2Symbol(c("PUMA","NOXA","BIM"))

richierocks/limma2 documentation built on May 27, 2019, 8:47 a.m.