getCurrentMaps: Get the current maps for correcting gene symbols

In HGNChelper: Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse 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 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. getCurrentHumanMap() for HGNC human gene symbols from genenames.org getCurrentMouseMap() for MGI mouse gene symbols from www.informatics.jax.org/downloads/reports/MGI_EntrezGene.rpt

Usage

getCurrentHumanMap()
getCurrentMouseMap()

Value

a 'data.frame' that can be used as the checkGeneSymbols "map" argument

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" 
## so that human-like capitalization corrections aren't made
checkGeneSymbols(c("Gm46568", "1-Feb"), map=new.mouse.table, species="mouse")

## End(Not run)

HGNChelper documentation built on Oct. 30, 2019, 9:41 a.m.