Package: Qploidy
Title: Estimation of Ploidy and Detection of Aneuploidy Using
        Genotyping Data
Version: 1.0.1
Authors@R: c(person(given='Cristiane', 
                    family='Taniguti', 
                    email = 'cht47@cornell.edu', 
                    role = c('cre', 'aut')),
             person(given='Jeekin', 
                    family='Lau', 
                    email = 'Jeekin.Lau@usda.gov', 
                    role = c('ctb')),
             person(given = "David",
                    family = "Byrne",
                    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 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)
Imports: dplyr, ggplot2, tidyr, vroom, ggpubr, multtest, vcfR, stringr
Encoding: UTF-8
URL: https://github.com/Cristianetaniguti/Qploidy
BugReports: https://github.com/Cristianetaniguti/Qploidy/issues
RoxygenNote: 7.3.2
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: 2025-04-29 13:15:56 UTC; cht47
Author: Cristiane Taniguti [cre, aut],
  Jeekin Lau [ctb],
  David Byrne [ctb],
  Oscar Riera-Lizarazu [ctb]
Maintainer: Cristiane Taniguti <cht47@cornell.edu>
Repository: CRAN
Date/Publication: 2025-05-01 10:40:05 UTC
Built: R 4.4.3; ; 2025-11-26 05:55:59 UTC; windows
