API for pegas
Population and Evolutionary Genetics Analysis System

Global functions
.TempletonProb Source code
.VCFconnection Source code
.bySNP Source code
.check.order.alleles Source code
.checkPloidy Source code
.diffHaplo.loci Source code
.drawAlternativeLinks Source code
.drawSymbolsHaploNet Source code
.eq13.Hurlbert1971 Source code
.getMETAvcf Source code
.labelSegmentsHaploNet Source code
.multinomialCoef Source code
.mutationRug Source code
.rotateSquares Source code
.setWindow4haploNet Source code
.sort.alleles Source code
.squarePegas Source code
F2 Man page Source code
F3 Man page Source code
F4 Man page Source code
Fst Man page Source code
H Man page Source code
H.default Man page Source code
H.loci Man page Source code
LD Man page Source code
LD2 Man page Source code
LDmap Man page Source code
LDscan Man page Source code
LDscan.DNAbin Man page Source code
LDscan.loci Man page Source code
MMD Man page Source code
R2.test Man page Source code
Rst Man page Source code
VCFheader Man page Source code
VCFlabels Man page Source code
VCFloci Man page Source code
[.haplotype Man page
[.loci Man page
all.equal.haploNet Man page Source code
alleles2loci Man page Source code
allelicrichness Man page Source code
amova Man page Source code
as.evonet.haploNet Man page Source code
as.igraph.haploNet Man page Source code
as.loci Man page Source code
as.loci.character Man page Source code
as.loci.data.frame Man page Source code
as.loci.factor Man page Source code
as.loci.genind Man page Source code
as.loci.matrix Man page Source code
as.network.haploNet Man page Source code
as.phylo.haploNet Man page Source code
bind.loci Man page
by.loci Man page Source code
cbind.loci Man page Source code
circle Source code
cophenetic.haploNet Man page Source code
diamond Source code
diffHaplo Man page Source code
dist.asd Man page Source code
dist.hamming Man page Source code
dist.haplotype.loci Man page Source code
edit.loci Man page Source code
expand.genotype Man page Source code
genind2loci Man page Source code
geoTrans Man page Source code
geoTrans2 Man page Source code
geod Man page Source code
getAllCombs Source code
getAlleles Man page Source code
getGenotypes Man page Source code
getHaploNetOptions Man page Source code
getINFO Man page Source code
getPhi Man page Source code
getPloidy Man page Source code
hap.div Man page Source code
hap.div.DNAbin Man page Source code
hap.div.haplotype Man page Source code
haploFreq Man page Source code
haploNet Man page Source code
haplotype Man page Source code
haplotype.DNAbin Man page Source code
haplotype.character Man page Source code
haplotype.loci Man page Source code
haplotype.numeric Man page Source code
heterozygosity Man page Source code
hw.test Man page
hw.test.genind Man page Source code
hw.test.loci Man page Source code
is.phased Man page Source code
is.snp Man page Source code
is.snp.VCFinfo Man page Source code
is.snp.loci Man page Source code
jaguar Man page
labels.haploNet Source code
lines.stairway Man page Source code
loci Man page
loci2SnpMatrix Man page Source code
loci2alleles Man page Source code
loci2genind Man page Source code
mjn Man page Source code
msn Man page Source code
mst Man page Source code
mutations Man page Source code
na.omit.loci Man page Source code
nuc.div Man page Source code
nuc.div.DNAbin Man page Source code
nuc.div.haplotype Man page Source code
pegas Man page
pegas-package Man page
plot.haploNet Man page Source code
plot.haplotype Man page Man page Source code
plot.haplotype.loci Man page Source code
plot.mjn Man page Source code
plot.spectrum Man page Source code
plot.stairway Man page Source code
plot.summary.loci Man page Source code
plot.sw Man page Source code
plotNetMDS Man page Source code
print.VCFinfo Man page Source code
print.amova Man page Source code
print.haploNet Man page Source code
print.haplotype Man page Source code
print.loci Man page Source code
print.summary.loci Man page Source code
proba.genotype Man page Source code
rangePOS Man page Source code
rarefactionplot Man page Source code
rbind.loci Man page Source code
read.gtx Man page Source code
read.loci Man page Source code
read.vcf Man page Source code
replot Man page Source code
rhost Man page Source code
rmst Man page Source code
rr.test Man page Source code
selectQUAL Man page Source code
setHaploNetOptions Man page Source code
site.spectrum Man page Source code
site.spectrum.DNAbin Man page Source code
site.spectrum.loci Man page Source code
sort.haplotype Man page Source code
square Source code
stairway Man page Source code
subset.haplotype Man page Source code
summary.haplotype Man page Source code
summary.loci Man page Source code
sw Man page Source code
sw.DNAbin Man page Source code
sw.default Man page Source code
tajima.test Man page Source code
theta.h Man page Source code
theta.k Man page Source code
theta.msat Man page Source code
theta.s Man page Source code
theta.s.DNAbin Man page Source code
theta.s.default Man page Source code
theta.tree Man page Source code
theta.tree.hetero Man page Source code
unphase Man page Source code
write.loci Man page Source code
write.pegas.amova Man page Source code
write.vcf Man page Source code
pegas documentation built on May 17, 2021, 9:08 a.m.