snprelate_ld {snplinkage}

Wrapper for snpgdsLDMat to compute r2

Description

Wrapper for snpgdsLDMat to compute r2

Usage

snprelate_ld(
  gdata,
  window_size = 0,
  min_r2 = 0,
  snps_idx = NULL,
  scans_idx = NULL,
  threads = 1,
  quiet = FALSE
)

Arguments

gdata

A GenotypeData object

window_size

Max number of SNPs in LD window, 0 for no window

min_r2

Minimum r2 value to report

snps_idx

Indices of snps to use

scans_idx

Indices of scans to use

threads

The number of threads to use

quiet

Whether to be quiet

Value

A data frame with columns SNP_A, SNP_B, R2 for r2 >= min_r2