Package: Qploidy
Title: Estimation of Ploidy and Detection of Aneuploidy Using
        Genotyping Data
Version: 1.5.4
Authors@R: c(person(given='Cristiane', 
                    family='Taniguti', 
                    email = 'ctaniguti@ufl.edu', 
                    role = c('cre', 'aut')),
             person(given='Jeekin', 
                    family='Lau', 
                    email = 'Jeekin.Lau@usda.gov', 
                    role = c('ctb')),
             person(given = "Oscar",
                    family = "Riera-Lizarazu",
                    role = c("ctb"))
             )
Description: Provides functions for estimating ploidy levels and detecting aneuploidy 
             in individuals using allele intensities or allele count data from high-throughput genotyping platforms, including 
             single nucleotide polymorphism (SNP) arrays and sequencing-based technologies. Implements method described 
             in Taniguti et al. (2025) <doi:10.1002/tpg2.70044> an extended version of the 'PennCNV' 
             signal standardization method by Wang et al. (2007) <doi:10.1101/gr.6861907> for higher ploidy 
             levels. Computes B-allele frequencies (BAF), z-scores, and identifies copy number variation patterns.
License: AGPL (>= 3)
Depends: R (>= 3.6.0)
biocViews:
Imports: dplyr, ggplot2, tidyr, vroom, ggpubr, multtest, vcfR, stringr,
        magrittr
Encoding: UTF-8
URL: https://github.com/Cristianetaniguti/Qploidy
BugReports: https://github.com/Cristianetaniguti/Qploidy/issues
RoxygenNote: 7.3.3
Suggests: covr, spelling, updog, rmdformats, knitr (>= 1.10),
        rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
Language: en-US
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-07-10 14:37:34 UTC; ctaniguti
Author: Cristiane Taniguti [cre, aut],
  Jeekin Lau [ctb],
  Oscar Riera-Lizarazu [ctb]
Maintainer: Cristiane Taniguti <ctaniguti@ufl.edu>
Repository: CRAN
Date/Publication: 2026-07-11 16:20:08 UTC
Built: R 4.6.1; ; 2026-08-23 04:41:14 UTC; windows
