thinSnps: Thin SNPs

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Thin SNPs

Description

Thin SNPs according to various methods: based on their index or based on their genomic coordinate.

Usage

thinSnps(method, threshold, snp.coords, only.chr = NULL)

Arguments

method	index or coord
threshold	keep every "threshold" SNPs (if method="index"), keep SNPs with more than "threshold" base pairs between them (if method="coord")
snp.coords	data.frame with SNP identifiers as row names, and two columns, "chr" and "coord" or "pos"; SNPs will be sorted according to their coordinates per chromosome (use gtools::mixedsort if you want to also sort chromosomes)
only.chr	identifier of a given chromosome

Value

vector of SNP identifiers

Author(s)

Timothee Flutre

See Also

pruneSnpsLd

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.