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

Functions

alleles2loci Man page
amova Man page
as.igraph.haploNet Man page
as.loci Man page
as.loci.character Man page
as.loci.data.frame Man page
as.loci.factor Man page
as.loci.genind Man page
as.network.haploNet Man page
bind.loci Man page
cbind.loci Man page
diffHaplo Man page
dist.haplotype.loci Man page
edit.loci Man page
expand.genotype Man page
Fst Man page
genind2loci Man page
geod Man page
geoTrans Man page
getAlleles Man page
getGenotypes Man page
getINFO Man page
getPloidy Man page
H Man page
haploFreq Man page
haploNet Man page
haplotype Man page
[.haplotype Man page
haplotype.DNAbin Man page
haplotype.loci Man page
heterozygosity Man page
hw.test Man page
hw.test.genind Man page
hw.test.loci Man page
is.phased Man page
is.snp Man page
is.snp.VCFinfo Man page
jaguar Man page
LD Man page
LD2 Man page
LDmap Man page
LDscan Man page
loci Man page
[.loci Man page
loci2genind Man page
MMD Man page
mst Man page
na.omit.loci Man page
nuc.div Man page
nuc.div.DNAbin Man page
nuc.div.haplotype Man page
pegas Man page
pegas-package Man page
plot.haploNet Man page
plot.haplotype Man page
plot.haplotype Man page
plot.haplotype.loci Man page
plot.spectrum Man page
plot.summary.loci Man page
print.amova Man page
print.haploNet Man page
print.haplotype Man page
print.loci Man page
print.summary.loci Man page
print.VCFinfo Man page
proba.genotype Man page
R2.test Man page
rangePOS Man page
rbind.loci Man page
read.gtx Man page
read.loci Man page
read.vcf Man page
replot Man page
rr.test Man page
selectQUAL Man page
site.spectrum Man page
sort.haplotype Man page
subset.haplotype Man page
summary.loci Man page
tajima.test Man page
theta.h Man page
theta.k Man page
theta.msat Man page
theta.s Man page
theta.s.default Man page
theta.s.DNAbin Man page
theta.tree Man page
VCFheader Man page
VCFlabels Man page
VCFloci Man page
write.loci Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.