pegas v0.14

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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 in pegas

Name Description
F4 F-Statistics From Patterson et al
allelicrichness Allelic Richness and Rarefaction Plots
LD Linkage Disequilibrium
alleles2loci Build Loci Object From Matrix of Alleles
all.equal.haploNet Compare Two Haplotype Networks
LDscan Multi-Locus Linkage Disequilibrium
MMD Mismatch Distribution
VCFloci Information From VCF Files
R2.test Ramos-Onsins--Rozas Test of Neutrality
Fst F-Statistics
geoTrans Manipulate Geographical Coordinates
diffHaplo Comparison Between Two Haplotypes
amova Analysis of Molecular Variance
dist.asd Allelic Sharing Distance
by.loci Summary by Population of Other Factor
as.loci Conversion Among Allelic Data Classes
geod Geodesic Distances
haplotype.loci Haplotype Extraction and Frequencies From Allelic Data
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
haploFreq Haplotype Frequencies With a Covariate
hap.div Haplotype Diversity
dist.hamming Hamming Distance
bind.loci Bind Loci Objects
haploNet Haplotype Networks
rr.test Tajima Relative Rate Test of Molecular Clock
haplotype Haplotype Extraction and Frequencies
site.spectrum Site Frequency Spectrum
stairway The Stairway Plot
plotNetMDS Plot Networks With MDS Layout
pegas-package Population and Evolutionary Genetics Analysis System
hw.test Test of Hardy--Weinberg Equilibrium
edit.loci Edit Allelic Data with R's Data Editor
na.omit.loci Missing Allelic Data
jaguar Jaguar Micro-Satellites
subset.haplotype Subsetting and Filtering Haplotypes
tajima.test Test of the Neutral Mutation Hypothesis
nuc.div Nucleotide Diversity
sw Sliding Windows
theta.h Population Parameter THETA using Homozygosity
summary.loci Print and Summaries of Loci Objects
mjn Median-Joining Network
theta.tree Population Parameter THETA Using Genealogy
mst Minimum Spanning Tree and Network
read.loci Read Allelic Data Files
theta.s Population Parameter THETA using Segregating Sites
read.vcf Read Variant Calling Format Files
replot Edit the Layout of a Haplotype Network
read.gtx Read Genetix Data Files
utilities Utily Functions for pegas
theta.k Population Parameter THETA using Expected Number of Alleles
write.loci Write Allelic Data Files
theta.msat Population Parameter THETA From Micro-Satellites
No Results!

Vignettes of pegas

Name
ReadingFiles.Rnw
pegas.bib
tata
titi
toto
tutu
tyty
No Results!

Last month downloads

Details

Date 2020-09-16
ZipData no
License GPL (>= 2)
URL http://ape-package.ird.fr/pegas.html
NeedsCompilation yes
Packaged 2020-09-16 10:01:47 UTC; paradis
Repository CRAN
Date/Publication 2020-09-16 14:10:02 UTC

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