convertGeneIds: Convert between gene ids

In SMITE: Significance-based Modules Integrating the Transcriptome and Epigenome

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.

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 < [e-mail] >

See Also

AnnotationDBI, Biomart

Examples

data(genes_for_conversiontest)

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

SMITE documentation built on Nov. 8, 2020, 5:14 p.m.