SplitVcfLd: Split VCF by Linkage Disequilibrium

In Simon-Coetzee/funcivar: Calculate overlaps and enrichment between genomic variants and genomic features or segmentations

Description

Splits a VCF file into foreground and background variant sets based upon a Linkage Disequilibrium cutoff

Usage

SplitVcfLd(vcf, ld = list(metric = "R.squared", cutoff = 0.8, maf =
  0.01), strict.subset = TRUE)

Arguments

vcf	an object of class VCF, particularly one that has been processed by CalcLD()
ld	a list containing three fields. These include: metric, either 'R.squared' or 'D.prime' cutoff, numeric between 0 and 1, the value of the metric upon which to perform the cutoff maf, numeric between 0 and 0.5, the minor allele frequency considered to be included in both foreground and background
strict.subset	boolean indicating if one wishes the foreground to be a strict subset of the background, or an independant set.

Value

a list of length 2 containing in the 'fg' slot the VCF object of the foreground SNPs, and the bg slot containing the VCF object of the background SNPs

Simon-Coetzee/funcivar documentation built on Aug. 2, 2021, 9:55 a.m.