A B C D E F G I L M P R S T U V W misc
| Absent | Accessor and Replacement Functions for "gendata" Objects | 
| Absent-method | Class "genbinary" | 
| Absent<- | Accessor and Replacement Functions for "gendata" Objects | 
| Absent<--method | Class "genbinary" | 
| alleleCorrelations | Assign Alleles to Isoloci Based on Distribution of Genotypes | 
| alleleDiversity | Retrieve and Count Unique Alleles | 
| AllopolyTutorialData | Simulated Allotetraploid Data | 
| assignClones | Group Individuals Based on a Distance Threshold | 
| Bruvo.distance | Genetic Distance Metric of Bruvo et al. | 
| Bruvo2.distance | Distance Measure of Bruvo et al. under Genome Loss and Addition | 
| calcFst | Estimate Population Differentiation Statistics | 
| calcPopDiff | Estimate Population Differentiation Statistics | 
| catalanAlleles | Sort Alleles into Isoloci | 
| deleteLoci | Remove Samples or Loci from an Object | 
| deleteLoci-method | Class "genambig" | 
| deleteLoci-method | Class "genbinary" | 
| deleteLoci-method | Class "gendata" | 
| deleteSamples | Remove Samples or Loci from an Object | 
| deleteSamples-method | Class "genambig" | 
| deleteSamples-method | Class "genbinary" | 
| deleteSamples-method | Class "gendata" | 
| Description | Accessor and Replacement Functions for "gendata" Objects | 
| Description-method | Class "gendata" | 
| Description<- | Accessor and Replacement Functions for "gendata" Objects | 
| Description<--method | Class "gendata" | 
| deSilvaFreq | Estimate Allele Frequencies with EM Algorithm | 
| editGenotypes | Edit Genotypes Using the Data Editor | 
| editGenotypes-method | Class "genambig" | 
| editGenotypes-method | Class "genbinary" | 
| estimatePloidy | Estimate Ploidies Based on Allele Counts | 
| estimatePloidy-method | Class "genambig" | 
| estimatePloidy-method | Class "genbinary" | 
| FCRinfo | Additional Data on Rubus Samples | 
| find.missing.gen | Find Missing Genotypes | 
| find.na.dist | Tools for Working With Pairwise Distance Arrays | 
| find.na.dist.not.missing | Tools for Working With Pairwise Distance Arrays | 
| fixloci | Internal Functions in polysat | 
| freq.to.genpop | Convert Allele Frequencies for Adegenet | 
| G | Internal Functions in polysat | 
| genambig-class | Class "genambig" | 
| genambig.to.genbinary | Convert Between Genotype Object Classes | 
| genbinary-class | Class "genbinary" | 
| genbinary.to.genambig | Convert Between Genotype Object Classes | 
| gendata-class | Class "gendata" | 
| gendata.to.genind | Convert Data to genind Format | 
| genIndex | Find All Unique Genotypes for a Locus | 
| genIndex-method | Find All Unique Genotypes for a Locus | 
| GENLIST | Internal Functions in polysat | 
| Genotype | Accessor and Replacement Functions for "gendata" Objects | 
| Genotype-method | Class "genambig" | 
| Genotype-method | Class "genbinary" | 
| Genotype<- | Accessor and Replacement Functions for "gendata" Objects | 
| Genotype<--method | Class "genambig" | 
| genotypeDiversity | Genotype Diversity Statistics | 
| genotypeProbs | Calculate Probabilities of Unambiguous Genotypes | 
| Genotypes | Accessor and Replacement Functions for "gendata" Objects | 
| Genotypes-method | Class "genambig" | 
| Genotypes-method | Class "genbinary" | 
| Genotypes<- | Accessor and Replacement Functions for "gendata" Objects | 
| Genotypes<--method | Class "genambig" | 
| Genotypes<--method | Class "genbinary" | 
| INDEXG | Internal Functions in polysat | 
| initialize-method | Class "genambig" | 
| initialize-method | Class "genbinary" | 
| initialize-method | Class "gendata" | 
| isMissing | Determine Whether Genotypes Are Missing | 
| isMissing-method | Class "genambig" | 
| isMissing-method | Class "genbinary" | 
| Loci | Accessor and Replacement Functions for "gendata" Objects | 
| Loci-method | Class "gendata" | 
| Loci<- | Accessor and Replacement Functions for "gendata" Objects | 
| Loci<--method | Class "genambig" | 
| Loci<--method | Class "genbinary" | 
| Loci<--method | Class "gendata" | 
| Lynch.distance | Calculate Band-Sharing Dissimilarity Between Genotypes | 
| meandist.from.array | Tools for Working With Pairwise Distance Arrays | 
| meandistance.matrix | Mean Pairwise Distance Matrix | 
| meandistance.matrix2 | Mean Pairwise Distance Matrix | 
| merge | Merge Two Genotype Objects into One | 
| merge-method | Merge Two Genotype Objects into One | 
| merge-methods | Merge Two Genotype Objects into One | 
| mergeAlleleAssignments | Merge Allele Assignment Matrices | 
| Missing | Accessor and Replacement Functions for "gendata" Objects | 
| Missing-method | Class "gendata" | 
| Missing<- | Accessor and Replacement Functions for "gendata" Objects | 
| Missing<--method | Class "genambig" | 
| Missing<--method | Class "genbinary" | 
| Missing<--method | Class "gendata" | 
| PIC | Polymorphic Information Content | 
| plCollapse | Accessor, Replacement, and Manipulation Functions for '"ploidysuper"' Objects | 
| plCollapse-method | Class '"ploidysuper"' and Subclasses | 
| pld | Accessor, Replacement, and Manipulation Functions for '"ploidysuper"' Objects | 
| pld-method | Class '"ploidysuper"' and Subclasses | 
| pld<- | Accessor, Replacement, and Manipulation Functions for '"ploidysuper"' Objects | 
| pld<--method | Class '"ploidysuper"' and Subclasses | 
| Ploidies | Accessor and Replacement Functions for "gendata" Objects | 
| Ploidies-method | Class "gendata" | 
| Ploidies<- | Accessor and Replacement Functions for "gendata" Objects | 
| Ploidies<--method | Class "gendata" | 
| ploidylocus-class | Class '"ploidysuper"' and Subclasses | 
| ploidymatrix-class | Class '"ploidysuper"' and Subclasses | 
| ploidyone-class | Class '"ploidysuper"' and Subclasses | 
| ploidysample-class | Class '"ploidysuper"' and Subclasses | 
| ploidysuper-class | Class '"ploidysuper"' and Subclasses | 
| plotParamHeatmap | Perform Allele Assignments across Entire Dataset | 
| plotSSAllo | Perform Allele Assignments across Entire Dataset | 
| PopInfo | Accessor and Replacement Functions for "gendata" Objects | 
| PopInfo-method | Class "gendata" | 
| PopInfo<- | Accessor and Replacement Functions for "gendata" Objects | 
| PopInfo<--method | Class "gendata" | 
| PopNames | Accessor and Replacement Functions for "gendata" Objects | 
| PopNames-method | Class "gendata" | 
| PopNames<- | Accessor and Replacement Functions for "gendata" Objects | 
| PopNames<--method | Class "gendata" | 
| PopNum | Accessor and Replacement Functions for "gendata" Objects | 
| PopNum-method | Class "gendata" | 
| PopNum<- | Accessor and Replacement Functions for "gendata" Objects | 
| PopNum<--method | Class "gendata" | 
| Present | Accessor and Replacement Functions for "gendata" Objects | 
| Present-method | Class "genbinary" | 
| Present<- | Accessor and Replacement Functions for "gendata" Objects | 
| Present<--method | Class "genbinary" | 
| processDatasetAllo | Perform Allele Assignments across Entire Dataset | 
| RANMUL | Internal Functions in polysat | 
| read.ATetra | Read File in ATetra Format | 
| read.GeneMapper | Read GeneMapper Genotypes Tables | 
| read.GenoDive | Import Genotype Data from GenoDive File | 
| read.POPDIST | Read Genotype Data in POPDIST Format | 
| read.SPAGeDi | Read Genotypes in SPAGeDi Format | 
| read.STRand | Read Genotypes Produced by STRand Software | 
| read.Structure | Read Genotypes and Other Data from a Structure File | 
| read.Tetrasat | Read Data from a TETRASAT Input File | 
| recodeAllopoly | Create a New 'genambig' Dataset with Loci Split into Isoloci | 
| reformatPloidies | Convert Ploidy Format of a Dataset | 
| Samples | Accessor and Replacement Functions for "gendata" Objects | 
| Samples-method | Class "gendata" | 
| Samples<- | Accessor and Replacement Functions for "gendata" Objects | 
| Samples<--method | Class "genambig" | 
| Samples<--method | Class "genbinary" | 
| Samples<--method | Class "gendata" | 
| SELFMAT | Internal Functions in polysat | 
| Shannon | Genotype Diversity Statistics | 
| show-method | Class "genambig" | 
| simAllopoly | Generate Simulated Datasets | 
| simgen | Randomly Generated Data for Learning polysat | 
| simpleFreq | Simple Allele Frequency Estimator | 
| Simpson | Genotype Diversity Statistics | 
| Simpson.var | Genotype Diversity Statistics | 
| summary-method | Class "genambig" | 
| summary-method | Class "genbinary" | 
| summary-method | Class "gendata" | 
| testAlGroups | Assign Alleles to Isoloci Based on Distribution of Genotypes | 
| testgenotypes | Rubus Genotype Data for Learning polysat | 
| Usatnts | Accessor and Replacement Functions for "gendata" Objects | 
| Usatnts-method | Class "gendata" | 
| Usatnts<- | Accessor and Replacement Functions for "gendata" Objects | 
| Usatnts<--method | Class "gendata" | 
| viewGenotypes | Print Genotypes to the Console | 
| viewGenotypes-method | Class "genambig" | 
| viewGenotypes-method | Class "genbinary" | 
| write.ATetra | Write Genotypes in ATetra Format | 
| write.freq.SPAGeDi | Create a File of Allele Frequencies for SPAGeDi | 
| write.GeneMapper | Write Genotypes to a Table Similarly to ABI GeneMapper | 
| write.GenoDive | Write a File in GenoDive Format | 
| write.POPDIST | Write Genotypes to a POPDIST File | 
| write.SPAGeDi | Write Genotypes in SPAGeDi Format | 
| write.Structure | Write Genotypes in Structure 2.3 Format | 
| write.Tetrasat | Write Genotype Data in Tetrasat Format | 
| .unal1loc | Internal Functions in polysat | 
| [-method | Class "genambig" | 
| [-method | Class "genbinary" | 
| [-method | Class "gendata" |