API for dartR
Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Global functions
.onAttach Source code
CritSam Source code
CritSam_Chi Source code
EffectiveNumberSamplesMLE Source code
FstDistPlotter Source code
FstDistPlotterAddBadCurve Source code
FstDistPlotterZoom Source code
G Source code
GenerateSamples Source code
IncompleteGammaFunction Source code
J Source code
J_largeK Source code
J_perm Source code
OutFLANKBadCurvePlotter Source code
WC_FST_Diploids_2Alleles Source code
WC_FST_FiniteSample_Diploids_2Alleles Source code
WC_FST_FiniteSample_Diploids_2Alleles_NoCorr Source code
WC_FST_FiniteSample_Haploids_2AllelesB_MCW Source code
WC_FST_FiniteSample_Haploids_2AllelesB_NoSamplingCorrection Source code
[,dartR,ANY,ANY,ANY-method Man page
averagePairWiseSimilarityH Source code
bandicoot.gl Man page
calcThreshold Source code
cbind.dartR Man page Source code
clumpp Source code
delta Source code
discrete_palette Source code
fstBarCalculator Source code
fstBarCalculatorNoCorr Source code
getFSTs_diploids Source code
getStephens Source code
get_best_permutation Source code
gi2gl Man page Source code
gl.He Man page Source code
gl.Ho Man page Source code
gl.LDNe Man page Source code
gl.alf Man page Source code
gl.amova Man page Source code
gl.assign.grm Man page Source code
gl.assign.mahalanobis Man page Source code
gl.assign.pa Man page Source code
gl.assign.pca Man page Source code
gl.basic.stats Man page Source code
gl.blast Man page Source code
gl.check.verbosity Man page Source code
gl.collapse Man page Source code
gl.compliance.check Man page Source code
gl.costdistances Man page Source code
gl.define.pop Man page Source code
gl.diagnostics.hwe Man page Source code
gl.diagnostics.sim Man page Source code
gl.dist.ind Man page Source code
gl.dist.pop Man page Source code
gl.drop.ind Man page Source code
gl.drop.loc Man page Source code
gl.drop.pop Man page Source code
gl.edit.recode.ind Man page Source code
gl.edit.recode.pop Man page Source code
gl.evanno Man page Source code
gl.fdsim Man page Source code
gl.filter.allna Man page Source code
gl.filter.callrate Man page Source code
gl.filter.hamming Man page Source code
gl.filter.heterozygosity Man page Source code
gl.filter.hwe Man page Source code
gl.filter.ld Man page Source code
gl.filter.locmetric Man page Source code
gl.filter.maf Man page Source code
gl.filter.monomorphs Man page Source code
gl.filter.overshoot Man page Source code
gl.filter.pa Man page Source code
gl.filter.parent.offspring Man page Source code
gl.filter.rdepth Man page Source code
gl.filter.reproducibility Man page Source code
gl.filter.secondaries Man page Source code
gl.filter.sexlinked Man page Source code
gl.filter.taglength Man page Source code
gl.fixed.diff Man page Source code
gl.fst.pop Man page Source code
gl.genleastcost Man page Source code
gl.grm Man page Source code
gl.grm.network Man page Source code
gl.hwe.pop Man page Source code
gl.ibd Man page Source code
gl.impute Man page Source code
gl.install.vanilla.dartR Man page Source code
gl.join Man page Source code
gl.keep.ind Man page Source code
gl.keep.loc Man page Source code
gl.keep.pop Man page Source code
gl.ld.distance Man page Source code
gl.ld.haplotype Man page Source code
gl.list.reports Man page Source code
gl.load Man page Source code
gl.make.recode.ind Man page Source code
gl.make.recode.pop Man page Source code
gl.map.interactive Man page Source code
gl.map.structure Man page Source code
gl.merge.pop Man page Source code
gl.nhybrids Man page Source code
gl.outflank Man page Source code
gl.pcoa Man page Source code
gl.pcoa.plot Man page Source code
gl.percent.freq Man page Source code
gl.play.history Man page Source code
gl.plot.heatmap Man page Source code
gl.plot.network Man page Source code
gl.plot.structure Man page Source code
gl.print.history Man page Source code
gl.print.reports Man page Source code
gl.propShared Man page Source code
gl.random.snp Man page Source code
gl.read.csv Man page Source code
gl.read.dart Man page Source code
gl.read.fasta Man page Source code
gl.read.silicodart Man page Source code
gl.read.vcf Man page Source code
gl.reassign.pop Man page Source code
gl.recalc.metrics Man page Source code
gl.recode.ind Man page Source code
gl.recode.pop Man page Source code
gl.rename.pop Man page Source code
gl.report.bases Man page Source code
gl.report.callrate Man page Source code
gl.report.diversity Man page Source code
gl.report.hamming Man page Source code
gl.report.heterozygosity Man page Source code
gl.report.hwe Man page Source code
gl.report.ld Man page Source code
gl.report.ld.map Man page Source code
gl.report.locmetric Man page Source code
gl.report.maf Man page Source code
gl.report.monomorphs Man page Source code
gl.report.overshoot Man page Source code
gl.report.pa Man page Source code
gl.report.parent.offspring Man page Source code
gl.report.rdepth Man page Source code
gl.report.reproducibility Man page Source code
gl.report.secondaries Man page Source code
gl.report.sexlinked Man page Source code
gl.report.taglength Man page Source code
gl.run.structure Man page Source code
gl.sample Man page Source code
gl.save Man page Source code
gl.select.colors Man page Source code
gl.select.shapes Man page Source code
gl.set.verbosity Man page Source code
gl.sfs Man page Source code
gl.sim.WF.run Man page Source code
gl.sim.WF.table Man page Source code
gl.sim.create_dispersal Man page Source code
gl.sim.emigration Man page Source code
gl.sim.ind Man page Source code
gl.sim.mutate Man page Source code
gl.sim.offspring Man page Source code
gl.smearplot Man page Source code
gl.sort Man page Source code
gl.spatial.autoCorr Man page Source code
gl.subsample.loci Man page Source code
gl.test.heterozygosity Man page Source code
gl.tree.nj Man page Source code
gl.write.csv Man page Source code
gl2bayescan Man page Source code
gl2bpp Man page Source code
gl2demerelate Man page Source code
gl2eigenstrat Man page Source code
gl2fasta Man page Source code
gl2faststructure Man page Source code
gl2gds Man page Source code
gl2genalex Man page Source code
gl2genepop Man page
gl2geno Man page Source code
gl2gi Man page Source code
gl2hiphop Man page Source code
gl2phylip Man page Source code
gl2plink Man page Source code
gl2related Man page Source code
gl2sa Man page Source code
gl2sfs Man page Source code
gl2shp Man page Source code
gl2snapp Man page Source code
gl2structure Man page Source code
gl2svdquartets Man page Source code
gl2treemix Man page Source code
gl2vcf Man page Source code
ind.count Source code
interactive_reference Man page Source code
interactive_sim_run Man page Source code
is.fixed Man page Source code
iterativeGreedy Source code
largeKGreedy Source code
matrix2gen Source code
mcl Source code
memoryGreedy Source code
merge_gl_fasta Source code
migration Source code
negLLdfFstTrim Source code
outputDFStarterNoCorr Source code
pOutlierFinderChiSqNoCorr Source code
pTwoSidedFromChiSq Source code
platy Man page
possums.gl Man page
q_equilibrium Source code
rbind.dartR Man page Source code
recomb Source code
reproduction Source code
s_alleles Source code
sample_genotype Source code
selection_fun Source code
store Source code
testset.gl Man page
testset.gs Man page
testset_SNPs_2Row Man page
testset_metadata Man page
testset_pop_recode Man page
theme_dartR Man page Source code
utils.assignment Man page Source code
utils.assignment_2 Man page Source code
utils.assignment_3 Man page Source code
utils.assignment_4 Man page Source code
utils.basic.stats Man page Source code
utils.check.datatype Man page Source code
utils.dart2genlight Man page Source code
utils.dist.binary Man page Source code
utils.dist.ind.snp Man page Source code
utils.flag.start Man page Source code
utils.hamming Man page Source code
utils.het.pop Man page Source code
utils.jackknife Man page Source code
utils.n.var.invariant Man page Source code
utils.outflank Man page Source code
utils.outflank.MakeDiploidFSTMat Man page Source code
utils.outflank.plotter Man page Source code
utils.pa.Chao Source code
utils.read.dart Man page Source code
utils.read.fasta Source code
utils.recalc.avgpic Man page Source code
utils.recalc.callrate Man page Source code
utils.recalc.freqhets Man page Source code
utils.recalc.freqhomref Man page Source code
utils.recalc.freqhomsnp Man page Source code
utils.recalc.maf Man page Source code
utils.reset.flags Man page Source code
utils.spautocor Man page Source code
utils.structure.evanno Man page
utils.structure.genind2gtypes Man page
utils.structure.run Man page
utils.transpose Source code
zzz Man page
dartR documentation built on June 8, 2023, 6:48 a.m.