snprelate_ld_select: Wrapper for snpgdsLDpruning to select Tag SNPs

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

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.

snplinkage documentation built on Sept. 11, 2024, 6:02 p.m.