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pegas (version 1.0)

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

5,565

Version

1.0

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

April 8th, 2021

Functions in pegas (1.0)

LDscan

Multi-Locus Linkage Disequilibrium
Fst

F-Statistics
all.equal.haploNet

Compare Two Haplotype Networks
MMD

Mismatch Distribution
F4

F-Statistics From Patterson et al
allelicrichness

Allelic Richness and Rarefaction Plots
alleles2loci

Build Loci Object From Matrix of Alleles
VCFloci

Information From VCF Files
LD

Linkage Disequilibrium
R2.test

Ramos-Onsins--Rozas Test of Neutrality
amova

Analysis of Molecular Variance
cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks
dist.asd

Allelic Sharing Distance
by.loci

Summary by Population or Other Factor
as.loci

Conversion Among Allelic Data Classes
dist.hamming

Hamming Distance
hw.test

Test of Hardy--Weinberg Equilibrium
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
diffHaplo

Comparison Between Two Haplotypes
haploNet

Haplotype Networks
haploFreq

Haplotype Frequencies With a Covariate
haplotype

Haplotype Extraction and Frequencies
geod

Geodesic Distances
hap.div

Haplotype Diversity
mutations

Plot Mutations on Networks
haplotype.loci

Haplotype Extraction and Frequencies From Allelic Data
mst

Minimum Spanning Tree and Network
getHaploNetOptions

Options to Plot haploNet Objects
edit.loci

Edit Allelic Data with R's Data Editor
pegas-package

Population and Evolutionary Genetics Analysis System
bind.loci

Bind Loci Objects
read.loci

Read Allelic Data Files
theta.h

Population Parameter THETA using Homozygosity
theta.k

Population Parameter THETA using Expected Number of Alleles
utilities

Utily Functions for pegas
theta.tree

Population Parameter THETA Using Genealogy
write.loci

Write Allelic Data Files
site.spectrum

Site Frequency Spectrum
read.vcf

Read Variant Calling Format Files
stairway

The Stairway Plot
subset.haplotype

Subsetting and Filtering Haplotypes
theta.msat

Population Parameter THETA From Micro-Satellites
summary.loci

Print and Summaries of Loci Objects
theta.s

Population Parameter THETA using Segregating Sites
geoTrans

Manipulate Geographical Coordinates
plotNetMDS

Plot Networks With MDS Layout
read.gtx

Read Genetix Data Files
sw

Sliding Windows
jaguar

Jaguar Micro-Satellites
tajima.test

Test of the Neutral Mutation Hypothesis
na.omit.loci

Missing Allelic Data
mjn

Median-Joining Network
nuc.div

Nucleotide Diversity
replot

Edit the Layout of a Haplotype Network
rr.test

Tajima Relative Rate Test of Molecular Clock