Package: pegas 1.3

pegas: Population and Evolutionary Genetics Analysis System

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Authors:Emmanuel Paradis [aut, cre, cph], Thibaut Jombart [aut, cph], Zhian N. Kamvar [aut, cph], Brian Knaus [aut, cph], Klaus Schliep [aut, cph], Alastair Potts [aut, cph], David Winter [aut, cph]

pegas_1.3.tar.gz
pegas_1.3.zip(r-4.5)pegas_1.3.zip(r-4.4)pegas_1.3.zip(r-4.3)
pegas_1.3.tgz(r-4.4-x86_64)pegas_1.3.tgz(r-4.4-arm64)pegas_1.3.tgz(r-4.3-x86_64)pegas_1.3.tgz(r-4.3-arm64)
pegas_1.3.tar.gz(r-4.5-noble)pegas_1.3.tar.gz(r-4.4-noble)
pegas_1.3.tgz(r-4.4-emscripten)pegas_1.3.tgz(r-4.3-emscripten)
pegas.pdf |pegas.html✨
pegas/json (API)
NEWS

# Install 'pegas' in R:
install.packages('pegas', repos = c('https://emmanuelparadis.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/emmanuelparadis/pegas.html/issues

Datasets:
  • jaguar - Jaguar Micro-Satellites

On CRAN:

7.50 score 18 packages 556 scripts 5.3k downloads 117 mentions 80 exports 5 dependencies

Last updated 11 months agofrom:535a3ea809. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-win-x86_64OKNov 19 2024
R-4.5-linux-x86_64OKNov 19 2024
R-4.4-win-x86_64OKNov 19 2024
R-4.4-mac-x86_64OKNov 19 2024
R-4.4-mac-aarch64OKNov 19 2024
R-4.3-win-x86_64OKNov 19 2024
R-4.3-mac-x86_64OKNov 19 2024
R-4.3-mac-aarch64OKNov 19 2024

Exports:alleles2lociallelicrichnessamovaas.igraph.haploNetas.locias.network.haploNetdiffHaplodist.asddist.hammingdist.haplotype.lociexpand.genotypeF2F3F4Fstgenind2locigeodgeoTransgeoTrans2getAllelesgetGenotypesgetHaploNetOptionsgetINFOgetPhigetPloidyHhap.divhaploFreqhaploNethaplotypeheterozygosityhw.testis.phasedis.snpLDLD2LDmapLDscanloci2allelesloci2genindloci2SnpMatrixmjnMMDmsnmstmutationsnuc.divnullAlleles2NAplotNetMDSproba.genotypeR2.testrangePOSrarefactionplotread.gtxread.lociread.vcfreplotrhostrmstrr.testRstselectQUALsetHaploNetOptionssite.spectrumstairwayswtajima.testtheta.htheta.ktheta.msattheta.stheta.treetheta.tree.heterounphaseVCFheaderVCFlabelsVCFlociwrite.lociwrite.pegas.amovawrite.vcf

Dependencies:apedigestlatticenlmeRcpp

Plotting Haplotype Networks

Rendered fromPlotHaploNet.Rnwusingutils::Sweaveon Nov 19 2024.

Last update: 2021-04-08
Started: 2021-04-08

Reading Files

Rendered fromReadingFiles.Rnwusingutils::Sweaveon Nov 19 2024.

Last update: 2023-12-14
Started: 2012-07-31

Readme and manuals

Help Manual

Help pageTopics
Population and Evolutionary Genetics Analysis Systempegas-package pegas
Compare Two Haplotype Networksall.equal.haploNet
Build Loci Object From Matrix of Allelesalleles2loci loci2alleles
Allelic Richness and Rarefaction Plotsallelicrichness rarefactionplot rhost
Analysis of Molecular Varianceamova getPhi print.amova write.pegas.amova
Conversion Among Allelic Data Classesas.loci as.loci.character as.loci.data.frame as.loci.factor as.loci.genind as.loci.matrix genind2loci loci2genind loci2SnpMatrix
Bind Loci Objectsbind.loci cbind.loci rbind.loci
Summary by Population or Other Factorby.loci
Cophenetic Matrix on Haplotype Networkscophenetic.haploNet
Comparison Between Two HaplotypesdiffHaplo
Allelic Sharing Distancedist.asd
Hamming Distancedist.hamming
Edit Allelic Data with R's Data Editoredit.loci
F-Statistics From Patterson et alF2 F3 F4
F-StatisticsFst Rst
Geodesic Distancesgeod
Manipulate Geographical CoordinatesgeoTrans geoTrans2
Options to Plot haploNet ObjectsgetHaploNetOptions setHaploNetOptions
Haplotype Diversityhap.div hap.div.DNAbin hap.div.haplotype
Haplotype Frequencies With a CovariatehaploFreq
Haplotype Networksas.evonet.haploNet as.igraph.haploNet as.network.haploNet as.phylo.haploNet haploNet plot.haploNet print.haploNet
Haplotype Extraction and Frequencieshaplotype haplotype.character haplotype.DNAbin haplotype.numeric plot.haplotype print.haplotype sort.haplotype summary.haplotype [.haplotype
Haplotype Extraction and Frequencies From Allelic Datadist.haplotype.loci haplotype.loci plot.haplotype.loci
Heterozygosity at a Locus Using Gene FrequenciesH H.default H.loci heterozygosity
Test of Hardy-Weinberg Equilibriumhw.test hw.test.genind hw.test.loci
Jaguar Micro-Satellitesjaguar
Linkage DisequilibriumLD LD2
Multi-Locus Linkage DisequilibriumLDmap LDscan LDscan.DNAbin LDscan.loci
Median-Joining Networkmjn plot.mjn
Mismatch DistributionMMD
Minimum Spanning Tree and Networkmsn mst rmst
Plot Mutations on Networksmutations
Missing Allelic Datana.omit.loci nullAlleles2NA
Nucleotide Diversitynuc.div nuc.div.DNAbin nuc.div.haplotype
Plot Networks With MDS LayoutplotNetMDS
Ramos-Onsins-Rozas Test of NeutralityR2.test
Read Genetix Data Filesread.gtx
Read Allelic Data Filesloci read.loci
Read Variant Calling Format Filesread.vcf write.vcf
Edit the Layout of a Haplotype Networkreplot
Tajima Relative Rate Test of Molecular Clockrr.test
Site Frequency Spectrumplot.spectrum site.spectrum site.spectrum.DNAbin site.spectrum.loci
The Stairway Plotlines.stairway plot.stairway stairway
Subsetting and Filtering Haplotypessubset.haplotype
Print and Summaries of Loci Objectsplot.summary.loci print.loci print.summary.loci summary.loci [.loci
Sliding Windowsplot.sw sw sw.default sw.DNAbin
Test of the Neutral Mutation Hypothesistajima.test
Population Parameter THETA using Homozygositytheta.h
Population Parameter THETA using Expected Number of Allelestheta.k
Population Parameter THETA From Micro-Satellitestheta.msat
Population Parameter THETA using Segregating Sitestheta.s theta.s.default theta.s.DNAbin
Population Parameter THETA Using Genealogytheta.tree theta.tree.hetero
Utily Functions for pegasexpand.genotype getAlleles getGenotypes getPloidy is.phased is.snp is.snp.loci proba.genotype unphase
Information From VCF FilesgetINFO is.snp.VCFinfo print.VCFinfo rangePOS selectQUAL VCFheader VCFlabels VCFloci
Write Allelic Data Fileswrite.loci