TajimaD: Tajima's D

In nspope/r2vcftools: An R interface for vcftools

Description

Calculate a genome-wide estimate of Tajima's D, and optionally use simulation from the neutral model to correct for bias due to a minor-allele-frequency filter and perform a significance test.

Usage

TajimaD(object, maf = 0, nboot = 0, nsim = 1000, ploidy = 2,
  use_vcftools_D = FALSE)

Arguments

object	an object of class "vcfLink"
maf	the minimum allele frequency allowed in the null model simulations, as a proportion; SNPs with frequency < MAF are excluded from the simulations. The data is also thinned using this criterion prior to calculating D.
nboot	the number of bootstrap replicates used to generate a confidence interval around D; if 0, no bootstrap is performed
nsim	the number of simulations from the null model, used to correct bias due to the MAF and to test the significance of D; if 0, no correction is performed
ploidy	the ploidy of the organism
use_vcftools_D	if TRUE, use the method for calculating D implemented in vcftools, which is biased when there is missing data. If FALSE (default), use an unbiased (and faster) method

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