calc_snp_assoc_mapping: Get the SNP association mapping from foundersnps database.

In churchill-lab/qtl2api: QTL2 API Library

Get the SNP association mapping from foundersnps database.

Description

Get the SNP association mapping from foundersnps database.

Usage

calc_snp_assoc_mapping(
  dataset,
  id,
  chrom,
  location,
  db_file,
  window_size = 5e+05,
  intcovar = NULL,
  cores = 0
)

Arguments

dataset	The dataset object.
id	The unique id in the dataset.
chrom	The chromosome.
location	Location on chromosome in base pairs.
db_file	Full path to the sqlite database file.
window_size	The size of the window to scan before and after location.
intcovar	The interactive covariate.
cores	Number of cores to use (0 = ALL).

Value

a 'tibble' with the following columns: snp, chr, pos, alleles, sdp, ensembl_gene, csq, index, interval, on_map, lod

churchill-lab/qtl2api documentation built on April 17, 2025, 3:27 a.m.