Estimate Kinship and FST under Arbitrary Population Structure

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Documentation for package ‘popkin’ version 1.3.23

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

popkin-package	A package for estimating kinship and FST under arbitrary population structure
admix_label_cols	Label ancestries based on best match to individual labels
admix_order_cols	Reorder admixture matrix columns
avg_kinship_subpops	Calculate a kinship matrix between subpopulations by averaging individual data
fst	Calculate FST from a population-level kinship matrix or vector of inbreeding coefficients
hgdp_subset	HGDP subset
inbr	Extract inbreeding coefficients from a kinship matrix
inbr_diag	Replace kinship diagonal with inbreeding coefficients
mean_kinship	Calculate the weighted mean kinship
n_eff	Calculates the effective sample size of the data
plot_admix	Make a structure/admixture plot
plot_phylo	Plot a 'phylo' tree object
plot_popkin	Visualize one or more kinship matrices and other related objects
popkin	Estimate kinship from a genotype matrix and subpopulation assignments
popkin_A	Compute popkin's 'A' and 'M' matrices from genotypes
popkin_af	Estimate coancestry from an allele frequency matrix and subpopulation assignments
popkin_A_min_subpops	Estimate the minimum expected value of a matrix 'A' using subpopulations
pwfst	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
_PACKAGE	A package for estimating kinship and FST under arbitrary population structure