pegas v0.14
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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.
Functions in pegas
| Name | Description | |
| F4 | F-Statistics From Patterson et al | |
| allelicrichness | Allelic Richness and Rarefaction Plots | |
| LD | Linkage Disequilibrium | |
| alleles2loci | Build Loci Object From Matrix of Alleles | |
| all.equal.haploNet | Compare Two Haplotype Networks | |
| LDscan | Multi-Locus Linkage Disequilibrium | |
| MMD | Mismatch Distribution | |
| VCFloci | Information From VCF Files | |
| R2.test | Ramos-Onsins--Rozas Test of Neutrality | |
| Fst | F-Statistics | |
| geoTrans | Manipulate Geographical Coordinates | |
| diffHaplo | Comparison Between Two Haplotypes | |
| amova | Analysis of Molecular Variance | |
| dist.asd | Allelic Sharing Distance | |
| by.loci | Summary by Population of Other Factor | |
| as.loci | Conversion Among Allelic Data Classes | |
| geod | Geodesic Distances | |
| haplotype.loci | Haplotype Extraction and Frequencies From Allelic Data | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| haploFreq | Haplotype Frequencies With a Covariate | |
| hap.div | Haplotype Diversity | |
| dist.hamming | Hamming Distance | |
| bind.loci | Bind Loci Objects | |
| haploNet | Haplotype Networks | |
| rr.test | Tajima Relative Rate Test of Molecular Clock | |
| haplotype | Haplotype Extraction and Frequencies | |
| site.spectrum | Site Frequency Spectrum | |
| stairway | The Stairway Plot | |
| plotNetMDS | Plot Networks With MDS Layout | |
| pegas-package | Population and Evolutionary Genetics Analysis System | |
| hw.test | Test of Hardy--Weinberg Equilibrium | |
| edit.loci | Edit Allelic Data with R's Data Editor | |
| na.omit.loci | Missing Allelic Data | |
| jaguar | Jaguar Micro-Satellites | |
| subset.haplotype | Subsetting and Filtering Haplotypes | |
| tajima.test | Test of the Neutral Mutation Hypothesis | |
| nuc.div | Nucleotide Diversity | |
| sw | Sliding Windows | |
| theta.h | Population Parameter THETA using Homozygosity | |
| summary.loci | Print and Summaries of Loci Objects | |
| mjn | Median-Joining Network | |
| theta.tree | Population Parameter THETA Using Genealogy | |
| mst | Minimum Spanning Tree and Network | |
| read.loci | Read Allelic Data Files | |
| theta.s | Population Parameter THETA using Segregating Sites | |
| read.vcf | Read Variant Calling Format Files | |
| replot | Edit the Layout of a Haplotype Network | |
| read.gtx | Read Genetix Data Files | |
| utilities | Utily Functions for pegas | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| write.loci | Write Allelic Data Files | |
| theta.msat | Population Parameter THETA From Micro-Satellites | |
| No Results! | ||
Vignettes of pegas
| Name | ||
| ReadingFiles.Rnw | ||
| pegas.bib | ||
| tata | ||
| titi | ||
| toto | ||
| tutu | ||
| tyty | ||
| No Results! | ||
Last month downloads
Details
| Date | 2020-09-16 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape-package.ird.fr/pegas.html |
| NeedsCompilation | yes |
| Packaged | 2020-09-16 10:01:47 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2020-09-16 14:10:02 UTC |
| depends | adegenet , ape (>= 5.3-11) , R (>= 3.2.0) |
| imports | graphics , methods , utils |
| suggests | rgl , snpStats |
| Contributors | Alastair Potts, Brian Knaus, Klaus Schliep, David Winter, Thibaut Jombart, Zhian N. Kamvar |
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