# Tools for Polyploid Microsatellite Analysis

## Documentation for package ‘polysat’ version 1.7-3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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
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"