polysat: Tools for Polyploid Microsatellite Analysis

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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.

Author
Lindsay V. Clark [aut, cre]
Date of publication
2016-11-05 23:58:05
Maintainer
Lindsay V. Clark <lvclark@illinois.edu>
License
GPL-2
Version
1.6-0
URLs

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

Files in this package

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