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pegas (version 0.10)

Population and Evolutionary Genetics Analysis System

Description

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.

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Version

Install

install.packages('pegas')

Monthly Downloads

4,359

Version

0.10

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

May 3rd, 2017

Functions in pegas (0.10)

all.equal.haploNet

Compare Two Haplotype Networks
alleles2loci

Build Loci Object From Matrix of Alleles
amova

Analysis of Molecular Variance
bind.loci

Bind Loci Objects
R2.test

Ramos-Onsins--Rozas Test of Neutrality
VCFloci

Information From VCF Files
geoTrans

Manipulate Geographic Coordinates
haplotype

Haplotype Extraction and Frequencies
LDscan

Multi-Locus Linkage Disequilibrium
MMD

Mismatch Distribution
dist.hamming

Hamming Distance
edit.loci

Edit Allelic Data with R's Data Editor
mst

Minimum Spanning Tree and Network
na.omit.loci

Missing Allelic Data
replot

Edit the Layout of a Haplotype Network
rr.test

Tajima Relative Rate Test of Molecular Clock
summary.loci

Print and Summaries of Loci Objects
tajima.test

Test of the Neutral Mutation Hypothesis
theta.msat

Population Parameter THETA From Micro-Satellites
theta.s

Population Parameter THETA using Segregating Sites
as.loci

Conversion Among Allelic Data Classes
diffHaplo

Comparison Between Two Haplotypes
jaguar

Jaguar Micro-Satellites
mjn

Median-Joining Network
haplotype.loci

Haplotype Extraction and Frequencies From Allelic Data
nuc.div

Nucleotide Diversity
pegas-package

Population and Evolutionary Genetics Analysis System
site.spectrum

Site Frequency Spectrum
write.loci

Write Allelic Data Files
subset.haplotype

Subsetting and Filtering Haplotypes
Fst

F-Statistics
LD

Linkage Disequilibrium
haploFreq

Haplotype Frequencies With a Covariate
haploNet

Haplotype Networks
geod

Geodesic Distances
heterozygosity

Heterozygosity at a Locus Using Gene Frequencies
hw.test

Test of Hardy--Weinberg Equilibrium
theta.h

Population Parameter THETA using Homozygosity
plotNetMDS

Plot Networks With MDS Layout
read.gtx

Read Genetix Data Files
read.loci

Read Allelic Data Files
read.vcf

Read Variant Calling Format Files
theta.k

Population Parameter THETA using Expected Number of Alleles
theta.tree

Population Parameter THETA Using Genealogy
utilities

Utily Functions for pegas