pegas v0.12

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

Vignettes of pegas

Name
ReadingFiles.Rnw
pegas.bib
tata
titi
toto
tutu
tyty
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Last month downloads

Details

Date 2019-10-04
ZipData no
License GPL (>= 2)
URL http://ape-package.ird.fr/pegas.html
NeedsCompilation yes
Packaged 2019-10-04 12:30:33 UTC; paradis
Repository CRAN
Date/Publication 2019-10-05 04:20:02 UTC

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