Package: polysat
Version: 1.7-8
Date: 2024-12-20
Title: Tools for Polyploid Microsatellite Analysis
Authors@R: c(person("Lindsay V.", "Clark", email = "Lindsay.Clark@seattlechildrens.org", role = c("aut", "cre"),
                    comment = c(ORCID = "0000-0002-3881-9252")),
             person("Alistair J.", "Hall", role = "ctb",
                    comment = c(ORCID = "0000-0001-9293-8909")),
             person("Handunnethi Nihal", "de Silva", role = "ctb"),
             person("Tyler William", "Smith", role = "ctb",
                    comment = c(ORCID = "0000-0001-7683-2653")))
Imports: methods, stats, utils, grDevices, graphics, Rcpp
Suggests: ade4, adegenet, ape
LinkingTo: Rcpp
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)
        <doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier
        (2017) <doi:10.1111/1755-0998.12639>.
License: GPL-2
URL: https://github.com/lvclark/polysat/wiki
Repository: https://lvclark.r-universe.dev
Date/Publication: 2024-12-20 20:49:36 UTC
RemoteUrl: https://github.com/lvclark/polysat
RemoteRef: HEAD
RemoteSha: 1bea7c88aa2b5da45fa74af6bcdf5e20faa68396
NeedsCompilation: yes
Packaged: 2026-06-24 10:59:24 UTC; root
Author: Lindsay V. Clark [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-3881-9252>),
  Alistair J. Hall [ctb] (ORCID: <https://orcid.org/0000-0001-9293-8909>),
  Handunnethi Nihal de Silva [ctb],
  Tyler William Smith [ctb] (ORCID:
    <https://orcid.org/0000-0001-7683-2653>)
Maintainer: Lindsay V. Clark <Lindsay.Clark@seattlechildrens.org>