Linkage: Calculate linkage disequillibrium between loci

In nspope/r2vcftools: An R interface for vcftools

Description

Given a "vcfLink" object, returns a data frame with pairwise p-values between loci, under the null hypothesis that the loci are not in linkage disequillibrium.

Usage

Linkage(object, ...)

## S4 method for signature 'vcfLink'
Linkage(object, type = c("geno-r2", "geno-chisq",
  "interchrom-geno-r2"), arguments = linkageOptions(), verbose = TRUE)

linkageOptions(min.r2 = NULL, ld.window = NULL, ld.window.bp = NULL,
  ld.window.min = NULL, ld.window.bp.min = NULL)

Arguments

object	an object of class "vcfLink"
type	the type of comparison to make. See vcftools manual.
arguments	optional arguments for vcftools as returned by linkageOptions, see vcftools manual.
verbose	print stdout from vcftools?

nspope/r2vcftools documentation built on Oct. 10, 2019, 2:06 a.m.