bigsnpr: snp_asGeneticPos – R documentation

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snp_asGeneticPos

Interpolate to genetic positions

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

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

`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".

The new vector of genetic positions.

Analysis of Massive SNP Arrays

v1.10.8

GPL-3

Authors

Florian Privé [aut, cre], Michael Blum [ths], Hugues Aschard [ths], Bjarni Jóhann Vilhjálmsson [ths]

Initial release

2022-07-05