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pegas (version 1.1)

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

4,947

Version

1.1

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

December 16th, 2021

Functions in pegas (1.1)

F4

F-Statistics From Patterson et al
alleles2loci

Build Loci Object From Matrix of Alleles
LD

Linkage Disequilibrium
allelicrichness

Allelic Richness and Rarefaction Plots
all.equal.haploNet

Compare Two Haplotype Networks
R2.test

Ramos-Onsins--Rozas Test of Neutrality
MMD

Mismatch Distribution
VCFloci

Information From VCF Files
LDscan

Multi-Locus Linkage Disequilibrium
Fst

F-Statistics
dist.asd

Allelic Sharing Distance
dist.hamming

Hamming Distance
geoTrans

Manipulate Geographical Coordinates
edit.loci

Edit Allelic Data with R's Data Editor
amova

Analysis of Molecular Variance
bind.loci

Bind Loci Objects
hap.div

Haplotype Diversity
geod

Geodesic Distances
diffHaplo

Comparison Between Two Haplotypes
cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks
haplotype.loci

Haplotype Extraction and Frequencies From Allelic Data
haplotype

Haplotype Extraction and Frequencies
haploFreq

Haplotype Frequencies With a Covariate
read.vcf

Read Variant Calling Format Files
read.loci

Read Allelic Data Files
haploNet

Haplotype Networks
by.loci

Summary by Population or Other Factor
na.omit.loci

Missing Allelic Data
nuc.div

Nucleotide Diversity
hw.test

Test of Hardy--Weinberg Equilibrium
as.loci

Conversion Among Allelic Data Classes
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
subset.haplotype

Subsetting and Filtering Haplotypes
mjn

Median-Joining Network
jaguar

Jaguar Micro-Satellites
getHaploNetOptions

Options to Plot haploNet Objects
summary.loci

Print and Summaries of Loci Objects
theta.tree

Population Parameter THETA Using Genealogy
sw

Sliding Windows
tajima.test

Test of the Neutral Mutation Hypothesis
pegas-package

Population and Evolutionary Genetics Analysis System
utilities

Utily Functions for pegas
site.spectrum

Site Frequency Spectrum
mst

Minimum Spanning Tree and Network
replot

Edit the Layout of a Haplotype Network
write.loci

Write Allelic Data Files
theta.msat

Population Parameter THETA From Micro-Satellites
stairway

The Stairway Plot
theta.s

Population Parameter THETA using Segregating Sites
mutations

Plot Mutations on Networks
read.gtx

Read Genetix Data Files
rr.test

Tajima Relative Rate Test of Molecular Clock
plotNetMDS

Plot Networks With MDS Layout
theta.h

Population Parameter THETA using Homozygosity
theta.k

Population Parameter THETA using Expected Number of Alleles