R: Population and Evolutionary Genetics Analysis System

# Population and Evolutionary Genetics Analysis System

## Documentation for package ‘pegas’ version 1.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N P R S T U V W misc

pegas-package | Population and Evolutionary Genetics Analysis System

## -- A --

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
as.evonet.haploNet | Haplotype Networks
as.igraph.haploNet | Haplotype Networks
as.loci | Conversion Among Allelic Data Classes
as.loci.character | Conversion Among Allelic Data Classes
as.loci.data.frame | Conversion Among Allelic Data Classes
as.loci.factor | Conversion Among Allelic Data Classes
as.loci.genind | Conversion Among Allelic Data Classes
as.loci.matrix | Conversion Among Allelic Data Classes
as.network.haploNet | Haplotype Networks
as.phylo.haploNet | Haplotype Networks

## -- B --

bind.loci | Bind Loci Objects
by.loci | Summary by Population or Other Factor

## -- C --

cbind.loci | Bind Loci Objects
cophenetic.haploNet | Cophenetic Matrix on Haplotype Networks

## -- D --

diffHaplo | Comparison Between Two Haplotypes
dist.asd | Allelic Sharing Distance
dist.hamming | Hamming Distance
dist.haplotype.loci | Haplotype Extraction and Frequencies From Allelic Data

## -- E --

edit.loci | Edit Allelic Data with R's Data Editor
expand.genotype | Utily Functions for pegas

## -- F --

F2 | F-Statistics From Patterson et al
F3 | F-Statistics From Patterson et al
F4 | F-Statistics From Patterson et al
Fst | F-Statistics

## -- G --

genind2loci | Conversion Among Allelic Data Classes
geod | Geodesic Distances
geoTrans | Manipulate Geographical Coordinates
geoTrans2 | Manipulate Geographical Coordinates
getAlleles | Utily Functions for pegas
getGenotypes | Utily Functions for pegas
getHaploNetOptions | Options to Plot haploNet Objects
getINFO | Information From VCF Files
getPhi | Analysis of Molecular Variance
getPloidy | Utily Functions for pegas

## -- H --

H | Heterozygosity at a Locus Using Gene Frequencies
H.default | Heterozygosity at a Locus Using Gene Frequencies
H.loci | Heterozygosity at a Locus Using Gene Frequencies
hap.div | Haplotype Diversity
hap.div.DNAbin | Haplotype Diversity
hap.div.haplotype | Haplotype Diversity
haploFreq | Haplotype Frequencies With a Covariate
haploNet | Haplotype Networks
haplotype | Haplotype Extraction and Frequencies
haplotype.character | Haplotype Extraction and Frequencies
haplotype.DNAbin | Haplotype Extraction and Frequencies
haplotype.loci | Haplotype Extraction and Frequencies From Allelic Data
haplotype.numeric | Haplotype Extraction and Frequencies
heterozygosity | Heterozygosity at a Locus Using Gene Frequencies
hw.test | Test of Hardy-Weinberg Equilibrium
hw.test.genind | Test of Hardy-Weinberg Equilibrium
hw.test.loci | Test of Hardy-Weinberg Equilibrium

## -- I --

is.phased | Utily Functions for pegas
is.snp | Utily Functions for pegas
is.snp.loci | Utily Functions for pegas
is.snp.VCFinfo | Information From VCF Files

## -- J --

jaguar | Jaguar Micro-Satellites

## -- L --

LD | Linkage Disequilibrium
LD2 | Linkage Disequilibrium
LDmap | Multi-Locus Linkage Disequilibrium
LDscan | Multi-Locus Linkage Disequilibrium
LDscan.DNAbin | Multi-Locus Linkage Disequilibrium
LDscan.loci | Multi-Locus Linkage Disequilibrium
lines.stairway | The Stairway Plot
loci | Read Allelic Data Files
loci2alleles | Build Loci Object From Matrix of Alleles
loci2genind | Conversion Among Allelic Data Classes
loci2SnpMatrix | Conversion Among Allelic Data Classes

## -- M --

mjn | Median-Joining Network
MMD | Mismatch Distribution
msn | Minimum Spanning Tree and Network
mst | Minimum Spanning Tree and Network
mutations | Plot Mutations on Networks

## -- N --

na.omit.loci | Missing Allelic Data
nuc.div | Nucleotide Diversity
nuc.div.DNAbin | Nucleotide Diversity
nuc.div.haplotype | Nucleotide Diversity
nullAlleles2NA | Missing Allelic Data

## -- P --

pegas | Population and Evolutionary Genetics Analysis System
plot.haploNet | Haplotype Networks
plot.haplotype | Haplotype Extraction and Frequencies
plot.haplotype.loci | Haplotype Extraction and Frequencies From Allelic Data
plot.mjn | Median-Joining Network
plot.spectrum | Site Frequency Spectrum
plot.stairway | The Stairway Plot
plot.summary.loci | Print and Summaries of Loci Objects
plot.sw | Sliding Windows
plotNetMDS | Plot Networks With MDS Layout
print.amova | Analysis of Molecular Variance
print.haploNet | Haplotype Networks
print.haplotype | Haplotype Extraction and Frequencies
print.loci | Print and Summaries of Loci Objects
print.summary.loci | Print and Summaries of Loci Objects
print.VCFinfo | Information From VCF Files
proba.genotype | Utily Functions for pegas

## -- R --

R2.test | Ramos-Onsins-Rozas Test of Neutrality
rangePOS | Information From VCF Files
rarefactionplot | Allelic Richness and Rarefaction Plots
rbind.loci | Bind Loci Objects
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
rhost | Allelic Richness and Rarefaction Plots
rmst | Minimum Spanning Tree and Network
rr.test | Tajima Relative Rate Test of Molecular Clock
Rst | F-Statistics

## -- S --

selectQUAL | Information From VCF Files
setHaploNetOptions | Options to Plot haploNet Objects
site.spectrum | Site Frequency Spectrum
site.spectrum.DNAbin | Site Frequency Spectrum
site.spectrum.loci | Site Frequency Spectrum
sort.haplotype | Haplotype Extraction and Frequencies
stairway | The Stairway Plot
subset.haplotype | Subsetting and Filtering Haplotypes
summary.haplotype | Haplotype Extraction and Frequencies
summary.loci | Print and Summaries of Loci Objects
sw | Sliding Windows
sw.default | Sliding Windows
sw.DNAbin | Sliding Windows

## -- T --

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.s.default | Population Parameter THETA using Segregating Sites
theta.s.DNAbin | Population Parameter THETA using Segregating Sites
theta.tree | Population Parameter THETA Using Genealogy
theta.tree.hetero | Population Parameter THETA Using Genealogy

## -- U --

unphase | Utily Functions for pegas

## -- V --

VCFheader | Information From VCF Files
VCFlabels | Information From VCF Files
VCFloci | Information From VCF Files

## -- W --

write.loci | Write Allelic Data Files
write.pegas.amova | Analysis of Molecular Variance
write.vcf | Read Variant Calling Format Files

## -- misc --

[.haplotype | Haplotype Extraction and Frequencies
[.loci | Print and Summaries of Loci Objects