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pegas

Population and Evolutionary Genetics Analysis System

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.

Functions (55)

F234

F-Statistics From Patterson et al

Fst

F-Statistics

Linkage Disequilibrium

LDscan

Multi-Locus Linkage Disequilibrium

MMD

Mismatch Distribution

R2.test

Ramos-Onsins–Rozas Test of Neutrality

VCFloci

Information From VCF Files

all.equal.haploNet

Compare Two Haplotype Networks

alleles2loci

Build Loci Object From Matrix of Alleles

allelicrichness

Allelic Richness and Rarefaction Plots

amova

Analysis of Molecular Variance

bind.loci

Bind Loci Objects

by.loci

Summary by Population or Other Factor

conversion

Conversion Among Allelic Data Classes

cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks

diffHaplo

Comparison Between Two Haplotypes

dist.asd

Allelic Sharing Distance

dist.hamming

Hamming Distance

edit.loci

Edit Allelic Data with R's Data Editor

geoTrans

Manipulate Geographical Coordinates

geod

Geodesic Distances

hap.div

Haplotype Diversity

haploFreq

Haplotype Frequencies With a Covariate

haploNet

Haplotype Networks

haplotype

Haplotype Extraction and Frequencies

haplotype.loci

Haplotype Extraction and Frequencies From Allelic Data

heterozygosity

Heterozygosity at a Locus Using Gene Frequencies

hw.test

Test of Hardy–Weinberg Equilibrium

jaguar

Jaguar Micro-Satellites

mjn

Median-Joining Network

mst

Minimum Spanning Tree and Network

mutations

Plot Mutations on Networks

na.omit.loci

Missing Allelic Data

nuc.div

Nucleotide Diversity

options_themes_haploNet

Options to Plot haploNet Objects

pegas-package

Population and Evolutionary Genetics Analysis System

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

replot

Edit the Layout of a Haplotype Network

rr.test

Tajima Relative Rate Test of Molecular Clock

site.spectrum

Site Frequency Spectrum

stairway

The Stairway Plot

subset.haplotype

Subsetting and Filtering Haplotypes

summary.loci

Print and Summaries of Loci Objects

Sliding Windows

tajima.test

Test of the Neutral Mutation Hypothesis

theta.h

Population Parameter THETA using Homozygosity

theta.k

Population Parameter THETA using Expected Number of Alleles

theta.msat

Population Parameter THETA From Micro-Satellites

theta.s

Population Parameter THETA using Segregating Sites

theta.tree

Population Parameter THETA Using Genealogy

utilities

Utily Functions for pegas

write.loci

Write Allelic Data Files

pegas

Population and Evolutionary Genetics Analysis System

v1.0

GPL (>= 2)

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut, cph] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut, cph] (<https://orcid.org/0000-0003-1665-4343>), Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut, cph] (<https://orcid.org/0000-0003-0919-7279>), David Winter [aut, cph] (<https://orcid.org/0000-0002-6165-0029>)

Initial release

2021-04-08

pegas

Functions (55)

pegas

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