Man pages for pegas
Population and Evolutionary Genetics Analysis System

alleles2lociBuild Loci Object From Matrix of Alleles
all.equal.haploNetCompare Two Haplotype Networks
amovaAnalysis of Molecular Variance
bind.lociBind Loci Objects
conversionConversion Among Allelic Data Classes
diffHaploComparison Between Two Haplotypes
dist.hammingHamming Distance
dist.snpAllelic Sharing Distance with SNPs
edit.lociEdit Allelic Data with R's Data Editor
geodGeodesic Distances
geoTransManipulate Geographic 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
na.omit.lociMissing Allelic Data
nuc.divNucleotide Diversity
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
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 July 13, 2018, 1:02 a.m.