API for adegenet
Exploratory Analysis of Genetic and Genomic Data

Global functions
$,SNPbin-method Man page
$,genind-method Man page
$,genlight-method Man page
$,genpop-method Man page
$<-,SNPbin-method Man page
$<-,genind-method Man page
$<-,genlight-method Man page
$<-,genpop-method Man page
,SNPbin-method Man page Man page Man page Man page Man page Man page Man page Man page
,genlight-method Man page Man page Man page Man page Man page Man page Man page Man page
.SNPbin2int Source code
.SNPbinset Source code
.addStrata Source code
.bin2raw Source code
.boot_dapc_pred Source code
.boot_group_sampler Source code
.check_info Source code
.compute.null.IC Source code
.compute.wss Source code
.dapcServer Source code
.drop_alleles Source code
.find.freq.hyb Source code
.find.parents Source code
.find.sub.clusters Man page Source code
.gen.valid Source code
.genind.valid Source code
.genlab Man page Source code
.genpop.valid Source code
.get.prop.pred Source code
.getHier Source code
.getStrata Source code
.get_pop_inds Source code
.get_slot Source code
.glPca2dudi Source code
.global.ll Source code
.group_sampler Source code
.hasUniquePloidy Source code
.internal_C_routines Man page
.listenToTheBrood Source code
.ll.genotype.diploid Source code
.ll.genotype.haploid Source code
.make_strata Source code
.nameStrata Source code
.not_enough_rows_warning Source code
.oldSNPbinset Source code
.onAttach Source code
.onLoad Source code
.orthobasis.listw Source code
.palette_parser Source code
.pop_combiner Source code
.raw2bin Source code
.rbind_strata Source code
.readExt Man page Source code
.render.server.info Source code
.rescale.ll.mat Source code
.rmspaces Man page Source code
.seppop_internal Source code
.setHier Source code
.setPop Source code
.setStrata Source code
.splitStrata Source code
.strata_incompatible_warning Source code
.subsetbin Source code
.tabGetter Source code
.test_existing_hier Source code
.tidy.hybrid.coef Source code
.tidy.pop.freq Source code
.valid.genind Man page
.write_mvmapper_output Source code
AIC.snapclust Man page Source code
AICc Man page Source code
AICc.snapclust Man page Source code
BIC.snapclust Man page Source code
CheckAllSeg Man page
DNAbin2genind Man page Source code
GLdotProd Man page
GLsumFreq Man page
GLsumInt Man page
H3N2 Man page
HWE.test.genind Man page Source code
Hs Man page Source code
Hs.test Man page Source code
KIC Man page Source code
KIC.snapclust Man page Source code
NA.posi Man page
NA.posi,SNPbin-method Man page
NA.posi,genlight-method Man page
SNPbin Man page
SNPbin-class Man page
USflu Man page
USflu.fasta Man page
[,SNPbin,ANY,ANY,ANY-method Man page
[,SNPbin,ANY,ANY-method Man page
[,SNPbin-method Man page
[,genind,ANY,ANY,ANY-method Man page
[,genind-method Man page
[,genlight,ANY,ANY,ANY-method Man page
[,genlight,ANY,ANY-method Man page
[,genlight-method Man page
[,genpop,ANY,ANY,ANY-method Man page
[,genpop-method Man page
[.haploGen Man page
a.score Man page Source code
addStrata Man page Source code
addStrata,genind-method Man page
addStrata,genlight-method Man page
addStrata<- Man page
addStrata<-,genind-method Man page
addStrata<-,genlight-method Man page
adegenet Man page
adegenet.package Man page
adegenetIssues Man page Source code
adegenetServer Man page Source code
adegenetTutorial Man page Source code
adegenetWeb Man page Source code
alignment2genind Man page Source code
alleles Man page
alleles,gen-method Man page
alleles,genind-method Man page
alleles,genlight-method Man page
alleles,genpop-method Man page
alleles<- Man page
alleles<-,gen-method Man page
alleles<-,genind-method Man page
alleles<-,genlight-method Man page
alleles<-,genpop-method Man page
any2col Man page Source code
as,SNPbin,integer-method Man page
as,SNPbin,numeric-method Man page
as,data.frame,genlight-method Man page
as,genind,data.frame-method Man page
as,genind,genpop-method Man page
as,genind,ktab-method Man page
as,genind,matrix-method Man page
as,genlight,data.frame-method Man page
as,genlight,list-method Man page
as,genlight,matrix-method Man page
as,genlight,snp.matrix-method Man page
as,genpop,data.frame-method Man page
as,genpop,ktab-method Man page
as,genpop,matrix-method Man page
as,integer,SNPbin-method Man page
as,list,genlight-method Man page
as,matrix,genlight-method Man page
as,numeric,SNPbin-method Man page
as,seqTrack,graphNEL-method Man page
as-method Man page
as.POSIXct.haploGen Man page Source code
as.SNPbin Man page
as.SNPbin,integer-method Man page
as.SNPbin,numeric-method Man page
as.data.frame.genind Man page Source code
as.data.frame.genlight Man page Source code
as.data.frame.genpop Man page Source code
as.genind Man page Source code
as.genlight Man page
as.genlight,data.frame-method Man page
as.genlight,list-method Man page
as.genlight,matrix-method Man page
as.genlight,snp.matrix-method Man page
as.genpop Man page Source code
as.genpop.genind Man page Source code
as.igraph.haploGen Man page Source code
as.igraph.seqTrack Man page Source code
as.integer.SNPbin Man page Source code
as.ktab.genind Man page Source code
as.ktab.genpop Man page Source code
as.lda Man page Source code
as.lda.dapc Man page Source code
as.list.genlight Man page Source code
as.matrix.genind Man page Source code
as.matrix.genlight Man page Source code
as.matrix.genpop Man page Source code
as.seqTrack.haploGen Man page Source code
assignplot Man page Source code
azur Man page
binIntToBytes Man page
bluepal Man page
bytesToBinInt Man page
bytesToInt Man page
c.SNPbin Man page Source code
callOrNULL-class Man page
cbind.SNPbin Man page Source code
cbind.genlight Man page Source code
charOrNULL-class Man page
checkType Man page Source code
chooseCN Man page Source code
chr Man page
chr,genlight-method Man page
chr<- Man page
chr<-,genlight-method Man page
chromosome Man page
chromosome,genlight-method Man page
chromosome<- Man page
chromosome<-,genlight-method Man page
coerce,SNPbin,integer-method Man page
coerce,data.frame,genlight-method Man page
coerce,genind,data.frame-method Man page
coerce,genind,genpop-method Man page
coerce,genind,ktab-method Man page
coerce,genind,matrix-method Man page
coerce,genlight,data.frame-method Man page
coerce,genlight,list-method Man page
coerce,genlight,matrix-method Man page
coerce,genlight,snp.matrix-method Man page
coerce,genpop,data.frame-method Man page
coerce,genpop,ktab-method Man page
coerce,genpop,matrix-method Man page
coerce,integer,SNPbin-method Man page
coerce,list,genlight-method Man page
coerce,matrix,genlight-method Man page
coerce,numeric,SNPbin-method Man page
coerce,seqTrack,graphNEL-method Man page
colorplot Man page Source code
colorplot.default Man page Source code
colorplot.spca Man page Source code
compoplot Man page Source code
compoplot.dapc Man page Source code
compoplot.matrix Man page Source code
compoplot.snapclust Man page Source code
coords.monmonier Man page Source code
corner Man page Source code
dapc Man page
dapc.data.frame Man page Source code
dapc.dudi Man page Source code
dapc.genind Man page Source code
dapc.genlight Man page Source code
dapc.matrix Man page Source code
dapcIllus Man page
deepseasun Man page
df2genind Man page Source code
dfOrNULL-class Man page
dim,genlight-method Man page
dist,genpop,ANY,ANY,ANY,missing-method Man page
dist.genpop Man page Source code
eHGDP Man page
export_to_mvmapper Man page Source code
export_to_mvmapper.dapc Man page Source code
export_to_mvmapper.default Man page Source code
export_to_mvmapper.dudi Man page Source code
export_to_mvmapper.spca Man page Source code
extract.PLINKmap Man page Source code
fac2col Man page Source code
factorOrNULL-class Man page
fasta2DNAbin Man page Source code
fasta2genlight Man page Source code
find.clusters Man page
find.clusters.data.frame Man page Source code
find.clusters.genind Man page Source code
find.clusters.genlight Man page Source code
find.clusters.matrix Man page Source code
findMutations Man page Source code
findMutations.DNAbin Man page Source code
flame Man page
formOrNULL-class Man page
funky Man page
gen-class Man page
gengraph Man page
gengraph.DNAbin Man page Source code
gengraph.default Man page Source code
gengraph.dist Man page Source code
gengraph.genind Man page Source code
gengraph.genpop Man page Source code
gengraph.matrix Man page Source code
genind Man page Source code
genind-class Man page
genind2df Man page Source code
genind2genpop Man page Source code
genlight Man page
genlight-class Man page
genpop Man page Source code
genpop-class Man page
get.likelihood Man page Source code
get.likelihood.seqTrack Man page Source code
glDotProd Man page Source code
glMean Man page Source code
glNA Man page Source code
glPca Man page Source code
glPlot Man page Source code
glSim Man page Source code
glSum Man page Source code
glVar Man page Source code
global.rtest Man page Source code
graphMutations Man page Source code
graphMutations.DNAbin Man page Source code
greenpal Man page
greypal Man page
haploGen Man page Source code
haploGen-class Man page
hier Man page Source code
hier,genind-method Man page
hier,genlight-method Man page
hier<- Man page
hier<-,genind-method Man page
hier<-,genlight-method Man page
hybridize Man page Source code
hybridpal Man page Source code
hybridtoy Man page
import2genind Man page Source code
inbreeding Man page Source code
indInfo-class Man page
indNames Man page
indNames,genind-method Man page
indNames,genlight-method Man page
indNames<- Man page
indNames<-,genind-method Man page
indNames<-,genlight-method Man page
initialize,SNPbin-method Man page
initialize,genind-method Man page
initialize,genind-methods Man page
initialize,genlight-method Man page
initialize,genpop-method Man page
initialize,genpop-methods Man page
intOrNULL-class Man page
intOrNum-class Man page
is.genind Man page Source code
is.genpop Man page Source code
isPoly Man page
isPoly,genind-method Man page
isPoly,genpop-method Man page
isPoly-methods Man page
ktab-class Man page
labels.haploGen Man page Source code
lightseasun Man page
listOrNULL-class Man page
loadingplot Man page
loadingplot.default Man page Source code
loadingplot.glPca Man page Source code
locFac Man page
locFac,gen-method Man page
locFac,genind-method Man page
locFac,genpop-method Man page
locNames Man page
locNames,gen-method Man page
locNames,genind-method Man page
locNames,genlight-method Man page
locNames,genpop-method Man page
locNames<- Man page
locNames<-,gen-method Man page
locNames<-,genind-method Man page
locNames<-,genlight-method Man page
locNames<-,genpop-method Man page
local.rtest Man page Source code
makefreq Man page
makefreq,genind-method Man page
makefreq,genind-methods Man page
makefreq,genpop-method Man page
makefreq,genpop-methods Man page
makefreq.genind Man page
makefreq.genpop Man page
microbov Man page
minorAllele Man page Source code
monmonier Man page Source code
nAll Man page
nAll,gen-method Man page
nAll,genind-method Man page
nAll,genpop-method Man page
nInd Man page
nInd,genind-method Man page
nInd,genlight-method Man page
nLoc Man page
nLoc,SNPbin-method Man page
nLoc,gen-method Man page
nLoc,genind-method Man page
nLoc,genlight-method Man page
nLoc,genpop-method Man page
nPop Man page
nPop,genind-method Man page
nPop,genlight-method Man page
nPop,genpop-method Man page
nameStrata Man page Source code
nameStrata,genind-method Man page
nameStrata,genlight-method Man page
nameStrata<- Man page
nameStrata<-,genind-method Man page
nameStrata<-,genlight-method Man page
names,SNPbin-method Man page
names,genind-method Man page
names,genlight-method Man page
names,genpop-method Man page
nancycats Man page
nb_shared_all Man page
num2col Man page Source code
old2new Man page
old2new_genind Man page Source code
old2new_genlight Man page Source code
old2new_genpop Man page Source code
optim.a.score Man page Source code
optimize.monmonier Man page Source code
other Man page
other,gen-method Man page
other,genind-method Man page
other,genlight-method Man page
other,genpop-method Man page
other<- Man page
other<-,gen-method Man page
other<-,genind-method Man page
other<-,genlight-method Man page
other<-,genpop-method Man page
pairDist Man page
pairDist.default Man page Source code
pairDistPlot Man page
pairDistPlot.DNAbin Man page Source code
pairDistPlot.default Man page Source code
pairDistPlot.dist Man page Source code
pairDistPlot.genind Man page Source code
pairDistPlot.matrix Man page Source code
ploidy Man page
ploidy,SNPbin-method Man page
ploidy,genind-method Man page
ploidy,genlight-method Man page
ploidy,genpop-method Man page
ploidy<- Man page
ploidy<-,SNPbin-method Man page
ploidy<-,genind-method Man page
ploidy<-,genlight-method Man page
ploidy<-,genpop-method Man page
plot,genlight,ANY-method Man page
plot,genlight-method Man page
plot.genlight Man page
plot.haploGen Man page Source code
plot.monmonier Man page Source code
plot.seqTrack Man page Source code
plot.spca Man page
plotHaploGen Man page Source code
plotSeqTrack Man page Source code
pop Man page
pop,genind-method Man page
pop,genlight-method Man page
pop<- Man page
pop<-,gen-method Man page
pop<-,genind-method Man page
pop<-,genlight-method Man page
popInfo-class Man page
popNames Man page
popNames,genind-method Man page
popNames,genlight-method Man page
popNames,genpop-method Man page
popNames<- Man page
popNames<-,genind-method Man page
popNames<-,genlight-method Man page
popNames<-,genpop-method Man page
position Man page
position,genlight-method Man page
position<- Man page
position<-,genlight-method Man page
predict.dapc Man page Source code
print,genind-method Man page
print,genindSummary-method Man page
print,genpopSummary-method Man page
print.dapc Man page Source code
print.genindSummary Man page Source code
print.genpopSummary Man page Source code
print.glPca Man page Source code
print.haploGen Man page Source code
print.monmonier Man page Source code
print.spca Man page Source code
propShared Man page Source code
propTyped Man page
propTyped,genind-method Man page
propTyped,genpop-method Man page
propTyped-methods Man page
rbind.genlight Man page Source code
read.PLINK Man page Source code
read.fstat Man page Source code
read.genepop Man page Source code
read.genetix Man page Source code
read.plink Man page
read.snp Man page Source code
read.structure Man page Source code
redpal Man page
repool Man page Source code
rupica Man page
sample.haploGen Man page Source code
scaleGen Man page
scaleGen,genind-method Man page
scaleGen,genpop-method Man page
scaleGen-methods Man page
scatter.dapc Man page Source code
scatter.glPca Man page Source code
screeplot.spca Man page Source code
seasun Man page
selPopSize Man page
selPopSize,ANY-method Man page
selPopSize,genind-method Man page
selPopSize-methods Man page
seploc Man page
seploc,ANY-method Man page
seploc,genind-method Man page
seploc,genlight-method Man page
seploc,genpop-method Man page
seploc-methods Man page
seppop Man page
seppop,ANY-method Man page
seppop,genind-method Man page
seppop,genlight-method Man page
seppop-methods Man page
seqTrack Man page Source code
seqTrack-class Man page
seqTrack.default Man page Source code
seqTrack.haploGen Man page Source code
seqTrack.matrix Man page Source code
setPop Man page Source code
setPop,genind-method Man page
setPop,genlight-method Man page
setPop<- Man page
setPop<-,genind-method Man page
setPop<-,genlight-method Man page
show,SNPbin-method Man page
show,genind-method Man page
show,genlight-method Man page
show,genpop-method Man page
showmekittens Man page Source code
sim2pop Man page
snapclust Man page Source code
snapclust.choose.k Man page Source code
snpposi.plot Man page Source code
snpposi.plot.DNAbin Man page Source code
snpposi.plot.integer Man page Source code
snpposi.plot.numeric Man page Source code
snpposi.test Man page Source code
snpposi.test.DNAbin Man page Source code
snpposi.test.integer Man page Source code
snpposi.test.numeric Man page Source code
snpzip Man page Source code
spca Man page
spca.data.frame Man page Source code
spca.default Man page Source code
spca.genind Man page Source code
spca.genpop Man page Source code
spca.matrix Man page Source code
spcaIllus Man page
spca_randtest Man page Source code
spectral Man page
splitStrata Man page Source code
splitStrata,genind-method Man page
splitStrata,genlight-method Man page
splitStrata<- Man page
splitStrata<-,genind-method Man page
splitStrata<-,genlight-method Man page
strata Man page Source code
strata,genind-method Man page
strata,genlight-method Man page
strata<- Man page
strata<-,genind-method Man page
strata<-,genlight-method Man page
summary,genind-method Man page
summary,genpop-method Man page
summary.dapc Man page Source code
summary.spca Man page
swallowtails Man page
tab Man page
tab,genind-method Man page
tab,genind-methods Man page
tab,genlight-method Man page
tab,genpop-method Man page
tab,genpop-methods Man page
tab.genind Man page
tab.genpop Man page
transp Man page Source code
truenames Man page
truenames,ANY-method Man page
truenames,genind-method Man page
truenames,genpop-method Man page
truenames-methods Man page
usflu Man page
usflu.fasta Man page
virid Man page
wasp Man page
xvalDapc Man page
xvalDapc.data.frame Man page
xvalDapc.default Man page Source code
xvalDapc.genind Man page Source code
xvalDapc.genlight Man page Source code
xvalDapc.matrix Man page
adegenet documentation built on July 18, 2021, 1:06 a.m.