get_LD_blocks: Get LD blocks

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

Get LD blocks

Description

Identify the LD block in which the lead SNP resides.

Usage

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

Arguments

query_dat	SNP-level data table.
ss	snpStats object or LD matrix containing r or r2 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.

Value

A list with the input data and LD matrix (r²).

Source

adjclust GitHub

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.