Map SNPs to genes: ABC

Source: R/map_snps2genes_abc.R

Map SNPs (both coding and non-coding) onto genes using an Activity-by-Contact (ABC) model.

map_snps2genes_abc(
  sumstats,
  ref_genome = "GRCh37",
  dataset = "Nasser2020",
  abc = NULL,
  nCores = 1,
  verbose = TRUE
)

Arguments

sumstats

GWAS summary statistics munged by format_sumstats.
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.
dataset

Which ABC model to import.
abc

Use a previously downloaded ABC data.table.
nCores

Number of cores to parallelise 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

References

Nasser et al. 2020, Nature

Fulco et al. 2019, Nature Fulco et al. 2019, GitHub

ABC models from multiple Engreitz Lab publications