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pegas (version 1.2)

Population and Evolutionary Genetics Analysis System

Description

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

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Version

Install

install.packages('pegas')

Monthly Downloads

4,923

Version

1.2

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

February 23rd, 2023

Functions in pegas (1.2)

all.equal.haploNet

Compare Two Haplotype Networks

Multi-Locus Linkage Disequilibrium

F-Statistics From Patterson et al

cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks

Hamming Distance

Comparison Between Two Haplotypes

Allelic Sharing Distance

Manipulate Geographical Coordinates

Edit Allelic Data with R's Data Editor

Analysis of Molecular Variance

Haplotype Networks

Haplotype Frequencies With a Covariate

Bind Loci Objects

Geodesic Distances

Summary by Population or Other Factor

Jaguar Micro-Satellites

Median-Joining Network

Haplotype Diversity

Plot Networks With MDS Layout

Haplotype Extraction and Frequencies From Allelic Data

Haplotype Extraction and Frequencies

Population and Evolutionary Genetics Analysis System

Missing Allelic Data

getHaploNetOptions

Options to Plot haploNet Objects

Site Frequency Spectrum

Test of the Neutral Mutation Hypothesis

Sliding Windows

Read Allelic Data Files

Read Variant Calling Format Files

Conversion Among Allelic Data Classes

Heterozygosity at a Locus Using Gene Frequencies

Nucleotide Diversity

Write Allelic Data Files

Edit the Layout of a Haplotype Network

Read Genetix Data Files

Population Parameter THETA Using Genealogy

The Stairway Plot

Utily Functions for pegas

Test of Hardy--Weinberg Equilibrium

Tajima Relative Rate Test of Molecular Clock

Population Parameter THETA using Homozygosity

Population Parameter THETA From Micro-Satellites

Population Parameter THETA using Expected Number of Alleles

Population Parameter THETA using Segregating Sites

Minimum Spanning Tree and Network

Plot Mutations on Networks

subset.haplotype

Subsetting and Filtering Haplotypes

Print and Summaries of Loci Objects

Linkage Disequilibrium

Build Loci Object From Matrix of Alleles

allelicrichness

Allelic Richness and Rarefaction Plots

Mismatch Distribution

Ramos-Onsins--Rozas Test of Neutrality

Information From VCF Files