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pegas (version 1.0-1)

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

4,923

Version

1.0-1

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

May 17th, 2021

Functions in pegas (1.0-1)

R2.test

Ramos-Onsins--Rozas Test of Neutrality
VCFloci

Information From VCF Files
all.equal.haploNet

Compare Two Haplotype Networks
amova

Analysis of Molecular Variance
bind.loci

Bind Loci Objects
haplotype.loci

Haplotype Extraction and Frequencies From Allelic Data
dist.hamming

Hamming Distance
allelicrichness

Allelic Richness and Rarefaction Plots
haplotype

Haplotype Extraction and Frequencies
dist.asd

Allelic Sharing Distance
geod

Geodesic Distances
na.omit.loci

Missing Allelic Data
hap.div

Haplotype Diversity
LD

Linkage Disequilibrium
replot

Edit the Layout of a Haplotype Network
F4

F-Statistics From Patterson et al
rr.test

Tajima Relative Rate Test of Molecular Clock
write.loci

Write Allelic Data Files
hw.test

Test of Hardy--Weinberg Equilibrium
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
LDscan

Multi-Locus Linkage Disequilibrium
Fst

F-Statistics
cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks
nuc.div

Nucleotide Diversity
geoTrans

Manipulate Geographical Coordinates
read.gtx

Read Genetix Data Files
diffHaplo

Comparison Between Two Haplotypes
by.loci

Summary by Population or Other Factor
edit.loci

Edit Allelic Data with R's Data Editor
getHaploNetOptions

Options to Plot haploNet Objects
jaguar

Jaguar Micro-Satellites
plotNetMDS

Plot Networks With MDS Layout
mjn

Median-Joining Network
site.spectrum

Site Frequency Spectrum
as.loci

Conversion Among Allelic Data Classes
stairway

The Stairway Plot
pegas-package

Population and Evolutionary Genetics Analysis System
theta.msat

Population Parameter THETA From Micro-Satellites
theta.s

Population Parameter THETA using Segregating Sites
theta.tree

Population Parameter THETA Using Genealogy
summary.loci

Print and Summaries of Loci Objects
mst

Minimum Spanning Tree and Network
haploFreq

Haplotype Frequencies With a Covariate
utilities

Utily Functions for pegas
subset.haplotype

Subsetting and Filtering Haplotypes
mutations

Plot Mutations on Networks
read.loci

Read Allelic Data Files
read.vcf

Read Variant Calling Format Files
haploNet

Haplotype Networks
theta.h

Population Parameter THETA using Homozygosity
sw

Sliding Windows
theta.k

Population Parameter THETA using Expected Number of Alleles
tajima.test

Test of the Neutral Mutation Hypothesis
alleles2loci

Build Loci Object From Matrix of Alleles
MMD

Mismatch Distribution