SMITE (version 1.0.2)

convertGeneIds: Convert between gene ids

Description

A convenient function used to convert between gene ids from different gene annotations.

Usage

convertGeneIds(gene_IDs, ID_type, ID_convert_to, delim = NULL, verbose = FALSE)

Arguments

gene_IDs

A vector of gene names.

ID_type

A character specifying the type of given annotation. Currently one of "refseq", "ensembleprot","uniprot" or "ensemble". In the case of ID_convert_to="entrez", "symbol"

ID_convert_to

A character specifying the type of desired annotation. Currently one of "symbol" or in they case of ID_type="symbol", "entrez"

delim

An optional character that will be removed from the beginning of each gene name. It can be a long string.

verbose

TRUE/FALSE Should the function be verbose? DEFAULTS to FALSE.

Value

A character vector formatted to ID_convert_to

Details

This is a very usefule function to efficently convert between gene ids. It currently relies on enumeration of each possible conversion, which has limited it's use to mainly converting to gene symbol.

See Also

AnnotationDBI, Biomart

Examples

data(genes_for_conversiontest)

genes[,1] <- convertGeneIds(gene_IDs=genes[,1], ID_type="refseq",
                            ID_convert_to="symbol")