pegas: Population and Evolutionary Genetics Analysis System

Share:

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.

Author
Emmanuel Paradis [aut, cre, cph], Thibaut Jombart [aut, cph], Klaus Schliep [aut, cph], Alastair Potts [aut, cph], David Winter [aut, cph]
Date of publication
2016-04-16 00:03:13
Maintainer
Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
License
GPL (>= 2)
Version
0.9
URLs

View on CRAN

Man pages

alleles2loci
Build Loci Object From Matrix of Alleles
amova
Analysis of Molecular Variance
bind.loci
Bind Loci Objects
conversion
Conversion Among Allelic Data Classes
diffHaplo
Comparison Between Two Haplotypes
edit.loci
Edit Allelic Data with R's Data Editor
Fst
F-Statistics
geod
Geodesic Distances
geoTrans
Manipulate Geographic Coordinates
haploFreq
Haplotype Frequencies With a Covariate
haploNet
Haplotype Networks
haplotype
Haplotype Extraction and Frequencies
haplotype.loci
Haplotype Extraction and Frequencies From Allelic Data
heterozygosity
Heterozygosity at a Locus Using Gene Frequencies
hw.test
Test of Hardy-Weinberg Equilibrium
jaguar
Jaguar Micro-Satellites
LD
Linkage Disequilibrium
LDscan
Multi-Locus Linkage Disequilibrium
MMD
Mismatch Distribution
mst
Minimum Spanning Tree
na.omit.loci
Missing Allelic Data
nuc.div
Nucleotide Diversity
pegas-package
Population and Evolutionary Genetics Analysis System
R2.test
Ramos-Onsins-Rozas Test of Neutrality
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
rr.test
Tajima Relative Rate Test of Molecular Clock
site.spectrum
Site Frequency Spectrum
subset.haplotype
Subsetting and Filtering Haplotypes
summary.loci
Print and Summaries of Loci Objects
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.tree
Population Parameter THETA Using Genealogy
utilities
Utily Functions for pegas
VCFloci
Information From VCF Files
write.loci
Write Allelic Data Files

Files in this package

pegas
pegas/inst
pegas/inst/CITATION
pegas/inst/doc
pegas/inst/doc/ReadingFiles.Rnw
pegas/inst/doc/ReadingFiles.pdf
pegas/inst/doc/ReadingFiles.R
pegas/src
pegas/src/Makevars
pegas/src/readVCFbin.c
pegas/src/pegas.c
pegas/NAMESPACE
pegas/NEWS
pegas/data
pegas/data/jaguar.rda
pegas/R
pegas/R/haplotype.R
pegas/R/geo.R
pegas/R/amova.R
pegas/R/nuc.div.R
pegas/R/tajima.test.R
pegas/R/plot.loci.R
pegas/R/hw.test.R
pegas/R/theta.R
pegas/R/conversion.R
pegas/R/rr.test.R
pegas/R/IO.R
pegas/R/Fst.R
pegas/R/VCFloci.R
pegas/R/R2.test.R
pegas/R/MMD.R
pegas/R/summary.loci.R
pegas/R/heterozygosity.R
pegas/R/site.spectrum.R
pegas/R/zzz.R
pegas/vignettes
pegas/vignettes/ReadingFiles.Rnw
pegas/vignettes/toto
pegas/vignettes/tyty
pegas/vignettes/pegas.bib
pegas/vignettes/tata
pegas/vignettes/titi
pegas/vignettes/tutu
pegas/MD5
pegas/build
pegas/build/vignette.rds
pegas/DESCRIPTION
pegas/man
pegas/man/edit.loci.Rd
pegas/man/R2.test.Rd
pegas/man/diffHaplo.Rd
pegas/man/LD.Rd
pegas/man/alleles2loci.Rd
pegas/man/haplotype.loci.Rd
pegas/man/utilities.Rd
pegas/man/VCFloci.Rd
pegas/man/nuc.div.Rd
pegas/man/theta.tree.Rd
pegas/man/theta.msat.Rd
pegas/man/jaguar.Rd
pegas/man/read.vcf.Rd
pegas/man/read.loci.Rd
pegas/man/replot.Rd
pegas/man/na.omit.loci.Rd
pegas/man/geoTrans.Rd
pegas/man/MMD.Rd
pegas/man/write.loci.Rd
pegas/man/hw.test.Rd
pegas/man/site.spectrum.Rd
pegas/man/theta.s.Rd
pegas/man/read.gtx.Rd
pegas/man/subset.haplotype.Rd
pegas/man/summary.loci.Rd
pegas/man/amova.Rd
pegas/man/haploNet.Rd
pegas/man/geod.Rd
pegas/man/mst.Rd
pegas/man/heterozygosity.Rd
pegas/man/conversion.Rd
pegas/man/haploFreq.Rd
pegas/man/theta.k.Rd
pegas/man/pegas-package.Rd
pegas/man/haplotype.Rd
pegas/man/theta.h.Rd
pegas/man/Fst.Rd
pegas/man/tajima.test.Rd
pegas/man/bind.loci.Rd
pegas/man/rr.test.Rd
pegas/man/LDscan.Rd