polysat v1.7-4

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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 and Polymorphic Information Content are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise or global differentiation statistics 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. polysat is described by Clark and Jasieniuk (2011) <doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2017) <doi:10.1111/1755-0998.12639>.

Functions in polysat

Name Description
Accessors Accessor and Replacement Functions for "gendata" Objects
genotypeProbs Calculate Probabilities of Unambiguous Genotypes
reformatPloidies Convert Ploidy Format of a Dataset
testgenotypes Rubus Genotype Data for Learning polysat
editGenotypes Edit Genotypes Using the Data Editor
gendata.to.genind Convert Data to genind Format
ploidysuper-class Class "ploidysuper" and Subclasses
AllopolyTutorialData Simulated Allotetraploid Data
calcPopDiff Estimate Population Differentiation Statistics
genambig.to.genbinary Convert Between Genotype Object Classes
alleleCorrelations Assign Alleles to Isoloci Based on Distribution of Genotypes
catalanAlleles Sort Alleles into Isoloci
assignClones Group Individuals Based on a Distance Threshold
Bruvo.distance Genetic Distance Metric of Bruvo et al.
estimatePloidy Estimate Ploidies Based on Allele Counts
genbinary-class Class "genbinary"
alleleDiversity Retrieve and Count Unique Alleles
read.GenoDive Import Genotype Data from GenoDive File
gendata-class Class "gendata"
read.POPDIST Read Genotype Data in POPDIST Format
deSilvaFreq Estimate Allele Frequencies with EM Algorithm
read.GeneMapper Read GeneMapper Genotypes Tables
FCRinfo Additional Data on Rubus Samples
Bruvo2.distance Distance Measure of Bruvo et al. under Genome Loss and Addition
meandist.from.array Tools for Working With Pairwise Distance Arrays
simpleFreq Simple Allele Frequency Estimator
deleteSamples Remove Samples or Loci from an Object
write.freq.SPAGeDi Create a File of Allele Frequencies for SPAGeDi
meandistance.matrix Mean Pairwise Distance Matrix
write.Tetrasat Write Genotype Data in Tetrasat Format
genambig-class Class "genambig"
genIndex Find All Unique Genotypes for a Locus
isMissing Determine Whether Genotypes Are Missing
merge-methods Merge Two Genotype Objects into One
viewGenotypes Print Genotypes to the Console
genotypeDiversity Genotype Diversity Statistics
pld Accessor, Replacement, and Manipulation Functions for "ploidysuper" Objects
simAllopoly Generate Simulated Datasets
mergeAlleleAssignments Merge Allele Assignment Matrices
plotSSAllo Perform Allele Assignments across Entire Dataset
simgen Randomly Generated Data for Learning polysat
Lynch.distance Calculate Band-Sharing Dissimilarity Between Genotypes
read.STRand Read Genotypes Produced by STRand Software
write.GeneMapper Write Genotypes to a Table Similarly to ABI GeneMapper
write.ATetra Write Genotypes in ATetra Format
recodeAllopoly Create a New genambig Dataset with Loci Split into Isoloci
read.SPAGeDi Read Genotypes in SPAGeDi Format
find.missing.gen Find Missing Genotypes
write.GenoDive Write a File in GenoDive Format
PIC Polymorphic Information Content
read.Structure Read Genotypes and Other Data from a Structure File
freq.to.genpop Convert Allele Frequencies for Adegenet
write.POPDIST Write Genotypes to a POPDIST File
write.Structure Write Genotypes in Structure 2.3 Format
read.ATetra Read File in ATetra Format
Internal Functions Internal Functions in polysat
read.Tetrasat Read Data from a TETRASAT Input File
write.SPAGeDi Write Genotypes in SPAGeDi Format
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Vignettes of polysat

Name
vignettebuild/AllopolyTutorialAssign.RData
vignettebuild/AllopolyTutorialDist.RData
vignettebuild/simfreq.txt
vignettebuild/simgenPloidies2.txt
vignettebuild/testmat.RData
vignettebuild/testmat2.RData
vignettebuild/testmat4.RData
vignettebuild/testmat5.RData
ATetraExample.txt
GeneMapperCBA15.txt
GeneMapperCBA23.txt
GeneMapperCBA28.txt
GeneMapperExample.txt
POPDISTexample1.txt
POPDISTexample2.txt
STRandExample.txt
allopolyVignette.Rnw
dominantExample.txt
genodiveExample.txt
polysattutorial.Rnw
spagediExample.txt
structureExample.txt
tetrasatExample.txt
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Details

Date 2019-03-03
LinkingTo Rcpp
License GPL-2
URL https://github.com/lvclark/polysat/wiki
NeedsCompilation yes
Packaged 2019-03-04 17:36:08 UTC; lvclark
Repository CRAN
Date/Publication 2019-03-06 22:10:12 UTC

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