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popkin (version 1.2.2)

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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Version

Install

install.packages('popkin')

Monthly Downloads

313

Version

1.2.2

License

GPL-3

Issues

2

Pull Requests

0

Stars

20

Forks

0

Maintainer

Alejandro Ochoa

Last Published

May 13th, 2019

Functions in popkin (1.2.2)

weightsSubpops-deprecated

Get weights for individuals that balance subpopulations
inbr_diag

Replace kinship diagonal with inbreeding coefficients
weights_subpops

Get weights for individuals that balance subpopulations
rescale_popkin

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

Validate a kinship matrix
pwfst

Estimate the individual-level pairwise FST matrix
rescalePopkin-deprecated

Rescale kinship matrix to set a given kinship value to zero.
popkin-package

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

Estimate kinship from a genotype matrix and subpopulation assignments
neff-deprecated

Calculates the effective sample size of the data
mean_kinship

Calculate the weighted mean kinship
plotPopkin-deprecated

Visualize one or more kinship matrices
n_eff

Calculates the effective sample size of the data
inbrDiag-deprecated

Replace kinship diagonal with inbreeding coefficients
plot_popkin

Visualize one or more kinship matrices
inbrDiag

Deprecated functions in package popkin.
fst

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

Extract inbreeding coefficients from a kinship matrix