get.nj: Generate a distance matrix for a SNP using fsts

In spflanagan/gwscaR: Genome-wide Selection Components Analysis in R

Description

Generate a distance matrix for a SNP using fsts

Usage

get.nj(vcf.row, pop.list)

Arguments

vcf.row	A row of a vcf file
pop.list	A list of populations in the order you want them to appear in the matrix

Value

fst.tree A neighbor-joining tree from the ape package

Examples

require(ape)
vcf.file<-system.file("extdata", "example.vcf.txt",package = "gwscaR")
vcf<-parse.vcf(vcf.file)
fst.trees<-list()
for(vcf.row in 1: nrow(vcf)){
  fst.trees<-c(fst.trees,get.nj(vcf[vcf.row,],pop.list=c("FEM","PRM","OFF")))
}

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