runLDPruning: TODO just a wrapper of snpgdsLDpruning

In belleau/aicsPaper: Accurate Inference of Genetic Ancestry from Cancer Sequencing

TODO just a wrapper of snpgdsLDpruning

Description

TODO

Usage

runLDPruning(
  gds,
  method = "corr",
  listSamples = NULL,
  listKeep = NULL,
  slide.max.bp.v = 5e+05,
  ld.threshold.v = sqrt(0.1),
  np = 1,
  verbose.v = FALSE
)

Arguments

gds	an object of class gds opened
method	the parameter method in SNPRelate::snpgdsLDpruning
listSamples	A vector of string corresponding to the sample.ids use in LDpruning
listKeep	the list of snp.id keep
slide.max.bp.v	TODO
ld.threshold.v	TODO
np	a single positive integer specifying the number of threads to be used. Default: 1.
verbose.v	a logical indicating if information is shown during the process. Default: FALSE.

Value

a list of SNP IDs stratified by chromosomes as generated by SNPRelate:snpgdsLDpruning().

Author(s)

Pascal Belleau, Astrid Deschênes and Alexander Krasnitz

Examples

## Path to the demo pedigree file is located in this package
data.dir <- system.file("extdata", package="RAIDS")

## TODO
gds <- "Demo GDS TODO"

belleau/aicsPaper documentation built on Aug. 4, 2022, 1:12 a.m.