pegas: Population and Evolutionary Genetics Analysis System

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.

AuthorEmmanuel Paradis [aut, cre, cph], Thibaut Jombart [aut, cph], Klaus Schliep [aut, cph], Alastair Potts [aut, cph], David Winter [aut, cph]
Date of publication2016-04-16 00:03:13
MaintainerEmmanuel Paradis <Emmanuel.Paradis@ird.fr>
LicenseGPL (>= 2)
Version0.9
http://ape-package.ird.fr/pegas.html

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

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