snp_asGeneticPos2: Download a genetic map

In bigsnpr: Analysis of Massive SNP Arrays

Download a genetic map

Description

This function uses linear interpolation, whereas snp_asGeneticPos() uses nearest neighbors.

Usage

download_genetic_map(
  type = c("hg19_OMNI", "hg19_hapmap", "hg38_price"),
  dir,
  ncores = 1
)

snp_asGeneticPos2(infos.chr, infos.pos, genetic_map)

Arguments

type	Which genetic map to download.
dir	Directory where to download and decompress files.
ncores	Number of cores used. Default doesn't use parallelism. You may use bigstatsr::nb_cores().
infos.chr	Vector of integers specifying each SNP's chromosome. Typically ⁠<bigSNP>$map$chromosome⁠.
infos.pos	Vector of integers specifying the physical position on a chromosome (in base pairs) of each SNP. Typically ⁠<bigSNP>$map$physical.pos⁠.
genetic_map	A data frame with 3 columns: chr, pos, and pos_cM. You can get it using download_genetic_map().

Details

The hg19 genetic maps are downloaded from https://github.com/joepickrell/1000-genomes-genetic-maps/ while the hg38 one is downloaded from ⁠https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/⁠.

Value

A data frame with 3 columns: chr, pos, and pos_cM.

The new vector of genetic positions.

bigsnpr documentation built on Sept. 30, 2024, 9:18 a.m.