Nei82Fst: Fst from hamming distance

In CMWbio/geaR: GDS Evolutionary Analysis in R

Fst from hamming distance

Description

Calculates sample size weighted or unweighted Fst-like \gammast from Nei (1982)

Usage

Nei82Fst(distMat, popList, pairs, ploidy, weighted = TRUE)

Arguments

distMat	hamming distance matrix calculated using the hidden function genoDist
popList	List of populations made from pops dataframe provided by users
pairs	list of populaiton pairs generated in getDiversityStats
ploidy	numeric number of chromosomes
weighted	logical Weight by sample subpopulaiton size. If TRUE mean nuceotide diversity within the subpopulaiton will be weigthed by sample size. With weighting 6 samples in p1 and 4 in p2, will result in 0.6*pi_p1 + 0.4*pi_p2 Alternatively, without weighting each subpopulaiton is assumed to contribute equally to the mean, (pi_p1 + pi_p2)/2

Details

Authours: Chris Ward Uses the mean nucleotide diversity within each subpopulaiton to calculate subpopulaiton pi and divides by the total nucleotide diversity.

Value

A dataframe Fst between two populations

CMWbio/geaR documentation built on April 22, 2023, 6:23 a.m.