Man pages for pegas
Population and Evolutionary Genetics Analysis System

alleles2lociBuild Loci Object From Matrix of Alleles
allelicrichnessAllelic Richness and Rarefaction Plots
all.equal.haploNetCompare Two Haplotype Networks
amovaAnalysis of Molecular Variance
bind.lociBind Loci Objects
by.lociSummary by Population or Other Factor
conversionConversion Among Allelic Data Classes
cophenetic.haploNetCophenetic Matrix on Haplotype Networks
diffHaploComparison Between Two Haplotypes
dist.asdAllelic Sharing Distance
dist.hammingHamming Distance
edit.lociEdit Allelic Data with R's Data Editor
F234F-Statistics From Patterson et al
geodGeodesic Distances
geoTransManipulate Geographical Coordinates
hap.divHaplotype Diversity
haploFreqHaplotype Frequencies With a Covariate
haploNetHaplotype Networks
haplotypeHaplotype Extraction and Frequencies
haplotype.lociHaplotype Extraction and Frequencies From Allelic Data
heterozygosityHeterozygosity at a Locus Using Gene Frequencies
hw.testTest of Hardy-Weinberg Equilibrium
jaguarJaguar Micro-Satellites
LDLinkage Disequilibrium
LDscanMulti-Locus Linkage Disequilibrium
mjnMedian-Joining Network
MMDMismatch Distribution
mstMinimum Spanning Tree and Network
mutationsPlot Mutations on Networks
na.omit.lociMissing Allelic Data
nuc.divNucleotide Diversity
options_themes_haploNetOptions to Plot haploNet Objects
pegas-packagePopulation and Evolutionary Genetics Analysis System
plotNetMDSPlot Networks With MDS Layout
R2.testRamos-Onsins-Rozas Test of Neutrality
read.gtxRead Genetix Data Files
read.lociRead Allelic Data Files
read.vcfRead Variant Calling Format Files
replotEdit the Layout of a Haplotype Network
rr.testTajima Relative Rate Test of Molecular Clock
site.spectrumSite Frequency Spectrum
stairwayThe Stairway Plot
subset.haplotypeSubsetting and Filtering Haplotypes
summary.lociPrint and Summaries of Loci Objects
swSliding Windows
tajima.testTest of the Neutral Mutation Hypothesis
theta.hPopulation Parameter THETA using Homozygosity
theta.kPopulation Parameter THETA using Expected Number of Alleles
theta.msatPopulation Parameter THETA From Micro-Satellites
theta.sPopulation Parameter THETA using Segregating Sites
theta.treePopulation Parameter THETA Using Genealogy
utilitiesUtily Functions for pegas
VCFlociInformation From VCF Files
write.lociWrite Allelic Data Files
pegas documentation built on March 7, 2023, 7:21 p.m.