snprelate_ld_select {snplinkage}

Wrapper for snpgdsLDpruning to select Tag SNPs

Description

The tagged snp set is (by sliding window) representative and strongly not redundant.

Usage

snprelate_ld_select(
  gdata,
  window_length = 500L,
  min_r2,
  window_size = NA,
  snps_idx = NULL,
  scans_idx = NULL,
  remove.monosnp = FALSE,
  autosome.only = FALSE,
  method = "r",
  threads = 1,
  quiet = FALSE,
  ...
)

Arguments

gdata

A GenotypeData object

window_length

Max length in kb of the window

min_r2

Minimum r2 value to report

window_size

Max number of SNPs in LD window

snps_idx

Indices of snps to use

scans_idx

Indices of scans to use

remove.monosnp

if TRUE, remove monomorphic SNPs

autosome.only

if TRUE, use autosomal SNPs only; if it is a numeric or character value, keep SNPs according to the specified chromosome

method

"composite", "r", "dprime", "corr", see details

threads

The number of threads to use, currently ignored

quiet

Whether to be quiet

...

Forwarded to SNPRelate::snpgdsLDpruning

Value

A list of SNP IDs stratified by chromosomes.