Identify the LD block in which the lead SNP resides

Source: R/get_LD_blocks.R

Identify the LD block in which the lead SNP resides

get_LD_blocks(
  dat,
  ss,
  stats = c("R.squared", "D.prime"),
  pct = 0.15,
  verbose = TRUE
)

Arguments

dat

SNP-level data table.
ss

snpStats object or LD matrix (containing r or r^2 values).
stats

a character vector specifying the linkage disequilibrium measures to be calculated (using the ld function) when x is a genotype matrix. Only "R.squared" and "D.prime" are allowed, see Details.
pct

minimum percentage of points for the plateau selection in capushe selection. See DDSE for further details
verbose

Print messages.

Source

adjclust GitHub

Value

A list with the input data and LD matrix (r^2),