ld_pruning: Prune dataset based on LD.

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Prune dataset based on LD.

Description

Used internally in radiator Prune dataset based on LD.

Usage

ld_pruning(ld.tibble = NULL, stats = NULL, ld.threshold = 0.8, verbose = TRUE)

Arguments

ld.tibble	(path) The markers LD pairwise data. Default: ld.tibble = NULL.
stats	(path) The markers missingness info statistics. Default: stats = NULL.
ld.threshold	(double) The threshold to prune SNPs in LD. Default: ld.threshold = 0.8.
verbose	(logical, optional) Default: verbose = TRUE.

Value

A list with blacklisted SNPs. Write the blacklist in the working directory.

Author(s)

Thierry Gosselin [e-mail]

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.