ld_missing: Prune dataset based on LD and missingness.

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

Prune dataset based on LD and missingness.

Description

Used internally in radiator Prune dataset based on LD, uses missingness to keep 1 SNP. This is the function that does it for 1 chrom. It's then used with purrr::map to run seriall on all chrom.

Usage

ld_missing(
  wl,
  data,
  ld.threshold = seq(0.1, 0.9, by = 0.1),
  denovo = NULL,
  ld.method = "r2",
  ld.figures = TRUE,
  path.folder = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE
)

Arguments

wl	The split dataset by chromosome.
data	The GDS object.
ld.threshold	The LD threshold.
denovo	de novo data or not ? (logical).
ld.method	The method to compute LD.
ld.figures	(logical, optional) Default: ld.figures = TRUE.
path.folder	(character) The path to the folder.
parallel.core	The number of CPU.
verbose	(logical, optional) Default: verbose = TRUE.

Value

A list with whitelists and blacklists of markers in LD.

Author(s)

Thierry Gosselin [e-mail]

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