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popkin

Estimate Kinship and FST under Arbitrary Population Structure

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 (2021) <doi:10.1371/journal.pgen.1009241>.

Functions (16)

fst

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

inbr

Extract inbreeding coefficients from a kinship matrix

Replace kinship diagonal with inbreeding coefficients

mean_kinship

Calculate the weighted mean kinship

Calculates the effective sample size of the data

Plot a phylo tree object

plot_popkin

Visualize one or more kinship matrices and other related objects

Estimate kinship from a genotype matrix and subpopulation assignments

popkin-package

A package for estimating kinship and FST under arbitrary population structure

Compute popkin's A and M matrices from genotypes

popkin_A_min_subpops

Estimate the minimum expected value of a matrix A using subpopulations

Estimate coancestry from an allele frequency matrix and subpopulation assignments

Estimate the individual-level pairwise FST matrix

rescale_popkin

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

validate_kinship

Validate a kinship matrix

weights_subpops

Get weights for individuals that balance subpopulations

popkin

Estimate Kinship and FST under Arbitrary Population Structure

v1.3.13

GPL-3

Authors

Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>), John D. Storey [aut] (<https://orcid.org/0000-0001-5992-402X>)

Initial release

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