snp_asGeneticPos {bigsnpr}

Interpolate to genetic positions

Description

Use genetic maps available at https://github.com/joepickrell/1000-genomes-genetic-maps/ to interpolate physical positions (in bp) to genetic positions (in cM).

Usage

snp_asGeneticPos(
  infos.chr,
  infos.pos,
  dir = tempdir(),
  ncores = 1,
  rsid = NULL,
  type = c("OMNI", "hapmap")
)

Arguments

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.

dir

Directory where to download and decompress files. Default is tempdir(). Directly use uncompressed files there if already present. You can use R.utils::gunzip() to uncompress local files.

ncores

Number of cores used. Default doesn't use parallelism. You may use nb_cores.

rsid

If providing rsIDs, the matching is performed using those (instead of positions) and variants not matched are interpolated using spline interpolation of variants that have been matched.

type

Whether to use the genetic maps interpolated from "OMNI" (the default), or from "hapmap".

Value

The new vector of genetic positions.