Population and Evolutionary Genetics Analysis System
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘pegas’ version 1.3
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 |