pre.cov: Generate LD files

In shuangsong0110/OWAS: Openness Weighted Association Studies: Leveraging Personal Genome Information to Prioritize Noncoding Variants

Generate LD files

Description

Using this function to generate blockwise LD matrix

Usage

pre.cov(ldpath = NULL, bedfile, path, chr = 1:22, shrink = T)

Arguments

ldpath	path for plink bfiles for the chromosome-wise LD reference;(e.g. 1000 Genome Project)
bedfile	path to the bedfile for OWAS segments (default: 100 KB up and down-stream of the TSS, the length of each segment is 5 KB)
path	specify the output path
chr	chromosome, can be a integer or vector from 1 to 22, default=1:22
shrink	shrink LD matrix or not, default=T

shuangsong0110/OWAS documentation built on April 2, 2024, 2:06 p.m.