get_lead_r2: Get LD with lead SNP

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

Get LD with lead SNP

Description

Add new columns r and r2 containing the degree of LD in each SNP (row) with the lead GWAS/QTL SNP.

Usage

get_lead_r2(
  dat,
  LD_matrix = NULL,
  fillNA = 0,
  LD_format = "matrix",
  verbose = TRUE
)

Arguments

dat	SNP-level data.
LD_matrix	LD matrix.
fillNA	Value to fill NAs with in r/r2 columns.
LD_format	The format of the provided LD_matrix: "matrix" (wide) or "df" (long).
verbose	Print messages.

Value

data.table with the columns r and r2.

Examples

dat2 <- echoLD::get_lead_r2(dat = echodata::BST1,
                            LD_matrix = echodata::BST1_LD_matrix)

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