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pegas (version 1.3)

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

5,541

Version

1.3

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

December 13th, 2023

Functions in pegas (1.3)

LDscan

Multi-Locus Linkage Disequilibrium
alleles2loci

Build Loci Object From Matrix of Alleles
R2.test

Ramos-Onsins--Rozas Test of Neutrality
F4

F-Statistics From Patterson et al
Fst

F-Statistics
VCFloci

Information From VCF Files
amova

Analysis of Molecular Variance
edit.loci

Edit Allelic Data with R's Data Editor
bind.loci

Bind Loci Objects
diffHaplo

Comparison Between Two Haplotypes
geoTrans

Manipulate Geographical Coordinates
by.loci

Summary by Population or Other Factor
dist.hamming

Hamming Distance
cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks
dist.asd

Allelic Sharing Distance
haploFreq

Haplotype Frequencies With a Covariate
mjn

Median-Joining Network
haploNet

Haplotype Networks
hap.div

Haplotype Diversity
haplotype.loci

Haplotype Extraction and Frequencies From Allelic Data
as.loci

Conversion Among Allelic Data Classes
jaguar

Jaguar Micro-Satellites
geod

Geodesic Distances
haplotype

Haplotype Extraction and Frequencies
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
read.vcf

Read Variant Calling Format Files
read.loci

Read Allelic Data Files
na.omit.loci

Missing Allelic Data
nuc.div

Nucleotide Diversity
plotNetMDS

Plot Networks With MDS Layout
subset.haplotype

Subsetting and Filtering Haplotypes
hw.test

Test of Hardy--Weinberg Equilibrium
read.gtx

Read Genetix Data Files
sw

Sliding Windows
summary.loci

Print and Summaries of Loci Objects
stairway

The Stairway Plot
tajima.test

Test of the Neutral Mutation Hypothesis
site.spectrum

Site Frequency Spectrum
getHaploNetOptions

Options to Plot haploNet Objects
theta.s

Population Parameter THETA using Segregating Sites
replot

Edit the Layout of a Haplotype Network
write.loci

Write Allelic Data Files
mutations

Plot Mutations on Networks
rr.test

Tajima Relative Rate Test of Molecular Clock
pegas-package

Population and Evolutionary Genetics Analysis System
mst

Minimum Spanning Tree and Network
theta.msat

Population Parameter THETA From Micro-Satellites
theta.h

Population Parameter THETA using Homozygosity
theta.k

Population Parameter THETA using Expected Number of Alleles
theta.tree

Population Parameter THETA Using Genealogy
utilities

Utily Functions for pegas
MMD

Mismatch Distribution
allelicrichness

Allelic Richness and Rarefaction Plots
LD

Linkage Disequilibrium
all.equal.haploNet

Compare Two Haplotype Networks