Tools for Polyploid Microsatellite Analysis
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘polysat’ version 1.7-7
Help Pages
A B C D E F G I L M P R S T U V W misc
-- A --
| 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 |
-- B --
| Bruvo.distance | Genetic Distance Metric of Bruvo et al. |
| Bruvo2.distance | Distance Measure of Bruvo et al. under Genome Loss and Addition |
-- C --
| calcFst | Estimate Population Differentiation Statistics |
| calcPopDiff | Estimate Population Differentiation Statistics |
| catalanAlleles | Sort Alleles into Isoloci |
-- D --
| 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 |
-- E --
| 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" |
-- F --
| 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 --
| 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" |
-- I --
| 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" |
-- L --
| 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 |
-- M --
| 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" |
-- P --
| 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 |
-- R --
| 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 |
-- S --
| 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" |
-- T --
| testAlGroups | Assign Alleles to Isoloci Based on Distribution of Genotypes |
| testgenotypes | Rubus Genotype Data for Learning polysat |
-- U --
| Usatnts | Accessor and Replacement Functions for "gendata" Objects |
| Usatnts-method | Class "gendata" |
| Usatnts<- | Accessor and Replacement Functions for "gendata" Objects |
| Usatnts<--method | Class "gendata" |
-- V --
| viewGenotypes | Print Genotypes to the Console |
| viewGenotypes-method | Class "genambig" |
| viewGenotypes-method | Class "genbinary" |
-- W --
| 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 |
-- misc --
| .unal1loc | Internal Functions in polysat |
| [-method | Class "genambig" |
| [-method | Class "genbinary" |
| [-method | Class "gendata" |