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polysat
View on CRAN: Click
here
Download and install polysat package within the R console
Install from CRAN:
install.packages("polysat")
Install from Github:
library("remotes")
install_github("cran/polysat")
Install by package version:
library("remotes")
install_version("polysat", "1.7-7")
Attach the package and use:
library("polysat")
Maintained by
Lindsay V. Clark
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2010-06-24
Latest Update: 2022-08-23
Description:
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)
and Clark and Schreier (2017)
.
How to cite:
Lindsay V. Clark (2010). polysat: Tools for Polyploid Microsatellite Analysis. R package version 1.7-7, https://cran.r-project.org/web/packages/polysat
Previous versions and publish date:
0.1 (2010-06-24 09:50), 1.0-1 (2010-10-19 09:31), 1.0 (2010-10-01 10:23), 1.1-0 (2010-12-07 09:21), 1.2-0 (2011-05-01 09:00), 1.2-1 (2012-01-15 10:27), 1.3-1 (2012-10-16 07:17), 1.3-2 (2013-09-06 06:36), 1.3-3 (2014-09-22 08:14), 1.4-0 (2015-06-13 14:56), 1.4-1 (2015-08-18 17:06), 1.5-0 (2016-07-18 13:28), 1.6-0 (2016-11-05 23:58), 1.7-0 (2017-05-03 08:14), 1.7-1 (2017-07-23 22:10), 1.7-2 (2017-08-17 20:09), 1.7-3 (2018-06-07 21:50), 1.7-4 (2019-03-06 23:10), 1.7-5 (2021-05-28 18:30), 1.7-6 (2021-12-08 14:30)
Other packages that cited polysat R package
View polysat citation profile
Other R packages that polysat depends,
imports, suggests or enhances
Functions, R codes and Examples using
the polysat R package
Some associated functions: AllopolyTutorialData . Bruvo.distance . Bruvo2.distance . FCRinfo . Lynch.distance . PIC . Samples . alleleCorrelations . alleleDiversity . assignClones . calcFst . catalanAlleles . deSilvaFreq . deleteSamples . editGenotypes . estimatePloidy . find.missing.gen . freq.to.genpop . genIndex . genambig-class . genambig.to.genbinary . genbinary-class . gendata-class . gendata.to.genind . genotypeDiversity . genotypeProbs . isMissing . meandist.from.array . meandistance.matrix . merge-methods . mergeAlleleAssignments . pld . ploidysuper-class . plotSSAllo . polysat-internal . read.ATetra . read.GeneMapper . read.GenoDive . read.POPDIST . read.SPAGeDi . read.STRand . read.Structure . read.Tetrasat . recodeAllopoly . reformatPloidies . simAllopoly . simgen . simpleFreq . testgenotypes . viewGenotypes . write.ATetra . write.GeneMapper . write.GenoDive . write.POPDIST . write.SPAGeDi . write.Structure . write.Tetrasat . write.freq.SPAGeDi .
Some associated R codes: RcppExports.R . allopolyploidy.R . class_conversion.R . classes_generics_methods.R . dataexport.R . dataimport.R . individual_distance.R . population_stats.R . Full polysat package functions and examples
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