pruningSample: TODO

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

TODO

Description

TODO

Usage

pruningSample(
  gds,
  method = "corr",
  sampleCurrent,
  study.id,
  listSNP = NULL,
  slide.max.bp.v = 5e+05,
  ld.threshold.v = sqrt(0.1),
  np = 1,
  verbose.v = FALSE,
  chr = NULL,
  minAF.SuperPop = NULL,
  keepGDSpruned = TRUE,
  PATHSAMPLEGDS = NULL,
  keepFile = FALSE,
  PATHPRUNED = ".",
  outPref = "pruned"
)

Arguments

gds	an object of class gds opened
method	a character string representing the method used in SNPRelate::snpgdsLDpruning() function. Default: "corr".
sampleCurrent	A character string corresponding to the sample.id use in LDpruning
study.id	A string corresponding to the study use in LDpruning
listSNP	the list of snp.id keep. TODO. Default: NULL.
slide.max.bp.v	a single numeric TODO. Default: 5e5.
ld.threshold.v	a single numeric TODO. Default: sqrt(0.1).
np	TODO. Default: 1.
verbose.v	TODO. Default: FALSE.
chr	TODO. Default: NULL.
minAF.SuperPop	TODO. Default: NULL.
keepGDSpruned	a boolean TODO. Default: TRUE.
PATHSAMPLEGDS	TODO
keepFile	a boolean indicating if the file must be TODO. Default: FALSE.
PATHPRUNED	a character string TODO. Default: ".".
outPref	TODO. Default: "pruned".

Value

The function returns 0L when successful.

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

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