Get MHC genes — get_mhc_genes • phenomix

Retrieve genes from the MHC (Major Histocompatibility Complex) region.

get_mhc_genes(
  seqnames = "chr6:25000000-34000000",
  ref_genome = "GRCh37",
  force_new = FALSE,
  verbose = TRUE
)

Arguments

seqnames	Genomic ranges to search for genes.
ref_genome	name of the reference genome used for the GWAS ("GRCh37" or "GRCh38"). Argument is case-insensitive. Default is NULL which infers the reference genome from the data.
force_new	Query for all genes within `seqnames` using TxDb.Hsapiens.UCSC.hg19.knownGene or TxDb.Hsapiens.UCSC.hg38.knownGene as a reference. If `FALSE` `(DEFAULT)`, will instead return a stored data.table aligned to the "GRCh37" reference genome.
verbose	Print messages.

Source

DeGAs

Details

The MHC region tends to be ubiquitously associated with all GWAS, so removing it allows us to focus on non-MHC signals of interest. For further information related to the MHC region, see the sources below.

Examples

MHC_genes <- get_mhc_genes()