fst.one.vcf: Calculate fsts from a single vcf

Description Usage Arguments Value

View source: R/gwscaR_fsts.R

Description

Calculate fsts from a single vcf

Usage

1
fst.one.vcf(vcf.row, group1, group2, cov.thresh = 0.2, maf = 0.05)

Arguments

vcf.row

A row of a data.frame in vcf format

group1

A list of individual names for pop1

group2

A list of individual names for pop2

cov.thresh

A proportion of individuals required for genotyping individuals (default is 0.2)

maf

A minimum allele frequency (default is 0.05)

Value

out A data.frame with columns: Hs1 (expected heterozygosity in pop 1), Hs2 (expected heterozygosity in pop2), Hs (expected heterozygosity within pops), Ht (expected heterozygosity between pops), Fst, NumAlleles, Num1 (number of individuals in pop1), and Num2 (number of individuals in pop2)


spflanagan/gwscaR documentation built on Nov. 14, 2019, 9:16 p.m.