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