polysat: Tools for Polyploid Microsatellite Analysis

A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi', 'POPDIST', 'STRand', and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise Fst values based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are also included for assigning alleles to isoloci in cases where one pair of microsatellite primers amplifies alleles from two or more independently segregating isoloci.

AuthorLindsay V. Clark [aut, cre]
Date of publication2016-11-05 23:58:05
MaintainerLindsay V. Clark <lvclark@illinois.edu>
LicenseGPL-2
Version1.6-0
https://github.com/lvclark/polysat/wiki

View on CRAN

Man pages

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

Bruvo2.distance: Distance Measure of Bruvo et al. under Genome Loss and...

Bruvo.distance: Genetic Distance Metric of Bruvo et al.

calcFst: Estimate Population Differentiation Statistics

catalanAlleles: Sort Alleles into Isoloci

deleteSamples: Remove Samples or Loci from an Object

deSilvaFreq: Estimate Allele Frequencies with EM Algorithm

editGenotypes: Edit Genotypes Using the Data Editor

estimatePloidy: Estimate Ploidies Based on Allele Counts

FCRinfo: Additional Data on Rubus Samples

find.missing.gen: Find Missing Genotypes

freq.to.genpop: Convert Allele Frequencies for Adegenet

genambig-class: Class "genambig"

genambig.to.genbinary: Convert Between Genotype Object Classes

genbinary-class: Class "genbinary"

gendata-class: Class "gendata"

gendata.to.genind: Convert Data to genind Format

genotypeDiversity: Genotype Diversity Statistics

genotypeProbs: Calculate Probabilities of Unambiguous Genotypes

isMissing: Determine Whether Genotypes Are Missing

Lynch.distance: Calculate Band-Sharing Dissimilarity Between Genotypes

meandistance.matrix: Mean Pairwise Distance Matrix

meandist.from.array: Tools for Working With Pairwise Distance Arrays

mergeAlleleAssignments: Merge Allele Assignment Matrices

merge-methods: Merge Two Genotype Objects into One

pld: Accessor, Replacement, and Manipulation Functions for...

ploidysuper-class: Class '"ploidysuper"' and Subclasses

plotSSAllo: Perform Allele Assignments across Entire Dataset

polysat-internal: 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

simAllopoly: Generate Simulated Datasets

simgen: Randomly Generated Data for Learning polysat

simpleFreq: Simple Allele Frequency Estimator

testgenotypes: Rubus Genotype Data for Learning polysat

viewGenotypes: Print Genotypes to the Console

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

Functions

Absent Man page
Absent<- Man page
Absent<-,genbinary-method Man page
Absent,genbinary-method Man page
alleleCorrelations Man page
alleleDiversity Man page
AllopolyTutorialData Man page
assignClones Man page
Bruvo2.distance Man page
Bruvo.distance Man page
calcFst Man page
calcPopDiff Man page
catalanAlleles Man page
deleteLoci Man page
deleteLoci,genambig-method Man page
deleteLoci,genbinary-method Man page
deleteLoci,gendata-method Man page
deleteSamples Man page
deleteSamples,genambig-method Man page
deleteSamples,genbinary-method Man page
deleteSamples,gendata-method Man page
Description Man page
Description<- Man page
Description<-,gendata-method Man page
Description,gendata-method Man page
deSilvaFreq Man page
editGenotypes Man page
editGenotypes,genambig-method Man page
editGenotypes,genbinary-method Man page
estimatePloidy Man page
estimatePloidy,genambig-method Man page
estimatePloidy,genbinary-method Man page
FCRinfo Man page
find.missing.gen Man page
find.na.dist Man page
find.na.dist.not.missing Man page
fixloci Man page
freq.to.genpop Man page
.G Man page
genambig-class Man page
[,genambig-method Man page
genambig.to.genbinary Man page
genbinary-class Man page
[,genbinary-method Man page
genbinary.to.genambig Man page
gendata-class Man page
[,gendata-method Man page
gendata.to.genind Man page
.genlist Man page
Genotype Man page
Genotype<- Man page
genotypeDiversity Man page
Genotype<-,genambig-method Man page
Genotype,genambig-method Man page
Genotype,genbinary-method Man page
genotypeProbs Man page
Genotypes Man page
Genotypes<- Man page
Genotypes<-,genambig-method Man page
Genotypes,genambig-method Man page
Genotypes<-,genbinary-method Man page
Genotypes,genbinary-method Man page
.indexg Man page
initialize,genambig-method Man page
initialize,genbinary-method Man page
initialize,gendata-method Man page
isMissing Man page
isMissing,genambig-method Man page
isMissing,genbinary-method Man page
Loci Man page
Loci<- Man page
Loci<-,genambig-method Man page
Loci<-,genbinary-method Man page
Loci<-,gendata-method Man page
Loci,gendata,missing,missing-method Man page
Loci,gendata,missing,numeric-method Man page
Loci,gendata,numeric,missing-method Man page
Loci,gendata,numeric,numeric-method Man page
Lynch.distance Man page
meandistance.matrix Man page
meandistance.matrix2 Man page
meandist.from.array Man page
merge Man page
mergeAlleleAssignments Man page
merge,genambig,genambig-method Man page
merge,genbinary,genbinary-method Man page
merge,gendata,gendata-method Man page
merge-methods Man page
Missing Man page
Missing<- Man page
Missing<-,genambig-method Man page
Missing<-,genbinary-method Man page
Missing<-,gendata-method Man page
Missing,gendata-method Man page
plCollapse Man page
plCollapse,ploidylocus,logical,logical-method Man page
plCollapse,ploidymatrix,logical,logical-method Man page
plCollapse,ploidyone,logical,logical-method Man page
plCollapse,ploidysample,logical,logical-method Man page
pld Man page
pld<- Man page
pld<-,ploidylocus-method Man page
pld,ploidylocus-method Man page
pld<-,ploidymatrix-method Man page
pld,ploidymatrix-method Man page
pld<-,ploidyone-method Man page
pld,ploidyone-method Man page
pld<-,ploidysample-method Man page
pld,ploidysample-method Man page
Ploidies Man page
Ploidies<- Man page
Ploidies<-,gendata-method Man page
Ploidies,gendata-method Man page
ploidylocus-class Man page
ploidymatrix-class Man page
ploidyone-class Man page
ploidysample-class Man page
ploidysuper-class Man page
plotParamHeatmap Man page
plotSSAllo Man page
PopInfo Man page
PopInfo<- Man page
PopInfo<-,gendata-method Man page
PopInfo,gendata-method Man page
PopNames Man page
PopNames<- Man page
PopNames<-,gendata-method Man page
PopNames,gendata-method Man page
PopNum Man page
PopNum<- Man page
PopNum<-,gendata,character-method Man page
PopNum,gendata,character-method Man page
Present Man page
Present<- Man page
Present<-,genbinary-method Man page
Present,genbinary-method Man page
processDatasetAllo Man page
.ranmul Man page
read.ATetra Man page
read.GeneMapper Man page
read.GenoDive Man page
read.POPDIST Man page
read.SPAGeDi Man page
read.STRand Man page
read.Structure Man page
read.Tetrasat Man page
recodeAllopoly Man page
reformatPloidies Man page
Samples Man page
Samples<- Man page
Samples<-,genambig-method Man page
Samples<-,genbinary-method Man page
Samples,gendata,character,missing-method Man page
Samples,gendata,character,numeric-method Man page
Samples<-,gendata-method Man page
Samples,gendata,missing,missing-method Man page
Samples,gendata,missing,numeric-method Man page
Samples,gendata,numeric,missing-method Man page
Samples,gendata,numeric,numeric-method Man page
.selfmat Man page
Shannon Man page
simAllopoly Man page
simgen Man page
simpleFreq Man page
Simpson Man page
Simpson.var Man page
summary,genambig-method Man page
summary,genbinary-method Man page
summary,gendata-method Man page
testAlGroups Man page
testgenotypes Man page
.unal1loc Man page
Usatnts Man page
Usatnts<- Man page
Usatnts<-,gendata-method Man page
Usatnts,gendata-method Man page
viewGenotypes Man page
viewGenotypes,genambig-method Man page
viewGenotypes,genbinary-method Man page
write.ATetra Man page
write.freq.SPAGeDi Man page
write.GeneMapper Man page
write.GenoDive Man page
write.POPDIST Man page
write.SPAGeDi Man page
write.Structure Man page
write.Tetrasat Man page

Files

polysat
polysat/inst
polysat/inst/CITATION
polysat/inst/extdata
polysat/inst/extdata/ATetraExample.txt
polysat/inst/extdata/STRandExample.txt
polysat/inst/extdata/POPDISTexample2.txt
polysat/inst/extdata/spagediExample.txt
polysat/inst/extdata/genodiveExample.txt
polysat/inst/extdata/structureExample.txt
polysat/inst/extdata/GeneMapperCBA23.txt
polysat/inst/extdata/dominantExample.txt
polysat/inst/extdata/GeneMapperCBA15.txt
polysat/inst/extdata/GeneMapperExample.txt
polysat/inst/extdata/POPDISTexample1.txt
polysat/inst/extdata/simgen.R
polysat/inst/extdata/GeneMapperCBA28.txt
polysat/inst/extdata/tetrasatExample.txt
polysat/inst/doc
polysat/inst/doc/allopolyVignette.R
polysat/inst/doc/polysattutorial.R
polysat/inst/doc/polysattutorial.Rnw
polysat/inst/doc/allopolyVignette.Rnw
polysat/inst/doc/allopolyVignette.pdf
polysat/inst/doc/polysattutorial.pdf
polysat/NAMESPACE
polysat/NEWS
polysat/data
polysat/data/AllopolyTutorialData.RData
polysat/data/FCRinfo.txt.gz
polysat/data/testgenotypes.RData
polysat/data/simgen.RData
polysat/R
polysat/R/population_stats.R polysat/R/dataexport.R polysat/R/dataimport.R polysat/R/classes_generics_methods.R polysat/R/allopolyploidy.R polysat/R/individual_distance.R polysat/R/class_conversion.R
polysat/vignettes
polysat/vignettes/vignettebuild
polysat/vignettes/vignettebuild/testmat2.RData
polysat/vignettes/vignettebuild/simgenPloidies2.txt
polysat/vignettes/vignettebuild/testmat5.RData
polysat/vignettes/vignettebuild/simfreq.txt
polysat/vignettes/vignettebuild/AllopolyTutorialAssign.RData
polysat/vignettes/vignettebuild/testmat4.RData
polysat/vignettes/vignettebuild/AllopolyTutorialDist.RData
polysat/vignettes/vignettebuild/testmat.RData
polysat/vignettes/polysattutorial.Rnw
polysat/vignettes/ATetraExample.txt
polysat/vignettes/allopolyVignette.Rnw
polysat/vignettes/STRandExample.txt
polysat/vignettes/POPDISTexample2.txt
polysat/vignettes/spagediExample.txt
polysat/vignettes/genodiveExample.txt
polysat/vignettes/structureExample.txt
polysat/vignettes/GeneMapperCBA23.txt
polysat/vignettes/dominantExample.txt
polysat/vignettes/GeneMapperCBA15.txt
polysat/vignettes/GeneMapperExample.txt
polysat/vignettes/POPDISTexample1.txt
polysat/vignettes/GeneMapperCBA28.txt
polysat/vignettes/tetrasatExample.txt
polysat/MD5
polysat/build
polysat/build/vignette.rds
polysat/DESCRIPTION
polysat/man
polysat/man/read.STRand.Rd polysat/man/catalanAlleles.Rd polysat/man/gendata-class.Rd polysat/man/read.POPDIST.Rd polysat/man/alleleCorrelations.Rd polysat/man/write.Structure.Rd polysat/man/alleleDiversity.Rd polysat/man/genambig.to.genbinary.Rd polysat/man/polysat-internal.Rd polysat/man/meandistance.matrix.Rd polysat/man/Samples.Rd polysat/man/Lynch.distance.Rd polysat/man/viewGenotypes.Rd polysat/man/simAllopoly.Rd polysat/man/read.SPAGeDi.Rd polysat/man/write.POPDIST.Rd polysat/man/write.freq.SPAGeDi.Rd polysat/man/recodeAllopoly.Rd polysat/man/Bruvo2.distance.Rd polysat/man/genambig-class.Rd polysat/man/freq.to.genpop.Rd polysat/man/simgen.Rd polysat/man/reformatPloidies.Rd polysat/man/write.Tetrasat.Rd polysat/man/deleteSamples.Rd polysat/man/assignClones.Rd polysat/man/read.Tetrasat.Rd polysat/man/ploidysuper-class.Rd polysat/man/FCRinfo.Rd polysat/man/write.GenoDive.Rd polysat/man/read.Structure.Rd polysat/man/mergeAlleleAssignments.Rd polysat/man/AllopolyTutorialData.Rd polysat/man/write.SPAGeDi.Rd polysat/man/editGenotypes.Rd polysat/man/deSilvaFreq.Rd polysat/man/genotypeProbs.Rd polysat/man/testgenotypes.Rd polysat/man/pld.Rd polysat/man/gendata.to.genind.Rd polysat/man/meandist.from.array.Rd polysat/man/isMissing.Rd polysat/man/genotypeDiversity.Rd polysat/man/Bruvo.distance.Rd polysat/man/merge-methods.Rd polysat/man/simpleFreq.Rd polysat/man/read.GeneMapper.Rd polysat/man/find.missing.gen.Rd polysat/man/genbinary-class.Rd polysat/man/write.GeneMapper.Rd polysat/man/read.GenoDive.Rd polysat/man/plotSSAllo.Rd polysat/man/read.ATetra.Rd polysat/man/calcFst.Rd polysat/man/write.ATetra.Rd polysat/man/estimatePloidy.Rd

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