Map SNPs to genes: txdb

Source: R/map_snps2genes_txdb.R

Map SNPs (both coding and non-coding) onto genes using TxDb.Hsapiens.UCSC.hg19.knownGene or TxDb.Hsapiens.UCSC.hg38.knownGene as a reference.

map_snps2genes_txdb(
  sumstats,
  promoter_upstream = 35000,
  promoter_downstream = 10000,
  queries = c("promoter", "coding", "intron", "threeUTR", "splicesite"),
  nCores = 1,
  verbose = TRUE
)

Arguments

sumstats

GWAS summary statistics munged by format_sumstats.
promoter_upstream

How many basepairs upstream of known promoters to search for genes.
promoter_downstream

How many basepairs dowmstream of known promoters to search for genes.
queries

Genomic region types to search for overlap with gr. See AllVariants for details.
nCores

Number of cores to parellelise across.
verbose

Print messages.
sumstats_file

GWAS summary statistics munged by format_sumstats. Can be a path to the saved file or data.table.
method

Method to use for mapping SNPs to genes.

Value

gene_hits data.table