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 |
