write.bed: Custom bed files

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

Custom bed files

Description

Using this function to generate blockwise LD matrix

Usage

write.bed(
  ldpath = NULL,
  path,
  type.len = "len",
  len = 5,
  type.gene = "gene",
  gene.region = NULL
)

Arguments

ldpath	path for plink bfiles for the chromosome-wise LD reference;(e.g. 1000 Genome Project)
path	specify the output path
type.len	'len'/'snp'
len	length (kb/number of SNPs)
type.gene	'gene'/'wg': by gene TSS or whole genome
gene.region	regulatory region of the gene (a data.frame with columns: V1(chr),V2(start),V3(end),V4(gene name))

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