Convert between gene ids

Description

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

Usage

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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.

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.

Value

A character vector formatted to ID_convert_to

Note

The function has enumerated combinations using AnnotationDBI. We can provide additional functionality if needed.

Author(s)

N. Ari Wijetunga < Neil.Wijetunga@med.einstein.yu.edu >

See Also

AnnotationDBI, Biomart

Examples

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data(genes_for_conversiontest)

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

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