pairwise.fst: Returns pairwise FST list for groups of individuals

In RADami: Phylogenetic Analysis of RADseq Data

Description

for use with RADami

Usage

pairwise.fst.loci(dat, group.list, to.do,
                  minInds = 3, do.hist = FALSE,
                  cores = 1, ...)

Arguments

dat	an object of class subset.pyRAD.loci
group.list	named list of character vectors, indicating groups of individuals
to.do	which groups to generate pairwise data for
minInds	minimum numer of individuals allowed per locus
do.hist	boolean; whether a histogram of pairwise FST should be written to the working directory
cores	how many processing cores to use
...	additional parameters passed along to genotypes.pyRAD.loci

Value

A list with the following elements:

fst	pairwise fst list
groups	groups used in the analysis
genotypes	genotype data
sp.pairs	species pairs analyzed
snpLocs	location of SNPs
timestamp	when analysis was conducted

Author(s)

Andrew Hipp

See Also

subset.pyRAD.loci

RADami documentation built on May 30, 2017, 8:23 a.m.