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popkin (version 1.0.5)

Estimate Kinship and FST under Arbitrary Population Structure

Description

Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2016) .

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Install

install.packages('popkin')

Monthly Downloads

313

Version

1.0.5

License

GPL-3

Issues

2

Pull Requests

0

Stars

20

Forks

0

Maintainer

Alejandro Ochoa

Last Published

January 26th, 2018

Functions in popkin (1.0.5)

popkin-package

A package for estimating kinship and FST under arbitrary population structure
popkin

Estimate kinship from a genotype matrix and subpopulation assignments
fst

Extract FST from a population-level kinship matrix or vector of inbreeding coefficients
inbr

Extract inbreeding coefficients from a kinship matrix
inbrDiag

Replace kinship diagonal with inbreeding coefficients
plotPopkin

Visualize one or more kinship matrices
weightsSubpops

Get weights for individuals that balance subpopulations
pwfst

Estimate the individual-level pairwise FST matrix
rescalePopkin

Rescale kinship matrix to set a given kinship value to zero.