getCurrentMaps: Get the current maps for correcting gene symbols

In HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols

Get the current maps for correcting gene symbols

Description

Valid human and mouse gene symbols can be updated frequently. Use these functions to get the most current lists of valid symbols, which you can then use as an input to the map argument of checkGeneSymbols. Make sure to change the default species="human" argument to checkGeneSymbols if you are doing this for mouse. Use getCurrentHumanMap for HGNC human gene symbols from https://www.genenames.org/ and getCurrentMouseMap for MGI mouse gene symbols from https://www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt.

Usage

getCurrentHumanMap()
getCurrentMouseMap()

Value

A data.frame that can be used for map argument of checkGeneSymbols function

Examples

## Not run: 
## human
new.hgnc.table <- getCurrentHumanMap()
checkGeneSymbols(c("3-Oct", "10-3", "tp53"), map=new.hgnc.table)

## mouse
new.mouse.table <- getCurrentMouseMap()
## Set species to NULL or "mouse" 
checkGeneSymbols(c("Gm46568", "1-Feb"), map=new.mouse.table, species="mouse")

## End(Not run)

HGNChelper documentation built on June 22, 2024, 7:03 p.m.