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hierfstat (version 0.5-11)

Estimation and Tests of Hierarchical F-Statistics

Description

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) ). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) .

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install.packages('hierfstat')

Monthly Downloads

5,190

Version

0.5-11

License

GPL (>= 2)

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Repository

https://github.com/jgx65/hierfstat

Homepage

https://www.r-project.org

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Last Published

May 5th, 2022

Functions in hierfstat (0.5-11)

Estimates pairwise kinships and individual inbreeding coefficients from dosage data

Estimates bootstrap confidence intervals for pairwise betas FST estimates

Estimates \(\beta\)s per population and a bootstrap confidence interval

Calculates corrected Assignment Index

Converts bi-allelic SNPs from hierfstat format to dosage format

Estimates Tajima's D

Performs bootstrapping over loci of population's Fis

allelic.richness

Estimates allelic richness

Basic diversity and differentiation statistics

A genetic dataset from a diploid organism in a continent-island model

Converts a Genetic Relationship Matrix (GRM) to a kinship matrix

Number of different alleles

Estimates pairwise FSTs according to Weir and Cockerham (1984)

Simulates genotypes in an island model at equilibrium

Principal coordinate analysis

Estimates nucleotide diversity (\(\pi\)) from dosage data

sim.genot.metapop.t

Simulate genetic data from a metapopulation model

Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland

Example data set with 4 levels, one diploid and one haploid locus

Genotypes and sex of 140 shrews Crocidura russula

A genetic dataset from a diploid organism in a continent-island model

Likelihood ratio G-statistic over loci

Converts a kinship matrix to a Genetic Relation Matrix (GRM)

Shifts a kinship matrix

Classical genetic distances estimation

Estimates F-statistics from dosage data

Converts diploid genotypic data into allelic data

Converts diploid genotypic data into allelic data

A genetic dataset from a diploid organism

Performs bootstrapping over loci of pairwise Fst

samp.between.within

Shuffles a sequence

Converts a hierfstat genetic data frame to dosage data

Creates a vector from a matrix

General information on the hierfstat package

individual counts

theta.Watt.dosage

Estimates \(\theta_{Watterson}\) from dosage data

Allelic frequencies

Estimates matching between pairs of individuals

Estimates variance components for each allele of a locus

Calculates likelihood-ratio G-statistic on contingency table

Import the output of the ms program in a BED object

Shuffles a sequence within groups defined by the input vector

Import ms output

Bootstrap confidence intervals for variance components

genind2hierfstat

Converts genind objects from adegenet into a hierfstat data frame

Estimates pairwise betas according to Weir and Goudet (2017)

pairwise.neifst

Estimates pairwise FSTs according to Nei (1987)

Computes Weir and Cockrham estimates of Fstatistics

Separates diploid genotypes in its constituant alleles

Writes a bayescan file

print function for pp.fst

Simulate data from a non equilibrium continent-island model

Read data generated by Hudson ms program Read data generated by Hudson ms program, either as Haplotypes or as SNPs.

wrapper to return per locus variance components

Shuffles a sequence among groups defined by the input vector

Converts a kinship matrix to a distance matrix

PCA on a matrix of individuals genotypes frequencies

Subsample a FSTAT data frame

Tests the significance of the effect of level on genetic differentiation

Tests the significance of the effect of inner.level on genetic differentiation within blocks defined by outer.level

Simulates frequencies, for internal use only

test.between.within

Tests the significance of the effect of test.lev on genetic differentiation

Test for sex biased dispersal

Write an Fstat data file

Tests the significance of the effect of test.lev on genetic differentiation

Reads a VCF file into a BED object

Example data set from Yang (1998) appendix

Read QuantiNemo extended format for genotype files Read QuantiNemo (http://www2.unil.ch/popgen/softwares/quantinemo/) genotype files extended format (option 2)

Reads data from a FSTAT file

Fills a triangular matrix from the inputed vector

read.fstat.data

Reads data from a FSTAT file

Write ped file for analyses with PLINK

Estimate variance components and hierarchical F-statistics over all loci

Write structure file