convertGeneIds {SMITE} | R Documentation

## 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.

### 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

    data(genes_for_conversiontest)

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

[Package SMITE version 1.8.0 Index]