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.
Version: 1.0.1 Depends: R (≥ 3.6.0) Imports: dplyr, ggplot2, tidyr, vroom, ggpubr, multtest, vcfR, stringr Suggests: covr, spelling, updog, rmdformats, knitr (≥ 1.10), rmarkdown, testthat (≥ 3.0.0) Published: 2025-05-01 DOI: 10.32614/CRAN.package.Qploidy Author: Cristiane Taniguti [cre, aut], Jeekin Lau [ctb], David Byrne [ctb], Oscar Riera-Lizarazu [ctb] Maintainer: Cristiane Taniguti <cht47 at cornell.edu> BugReports: https://github.com/Cristianetaniguti/Qploidy/issues License: AGPL (≥ 3) URL: https://github.com/Cristianetaniguti/Qploidy NeedsCompilation: no Language: en-US Citation: Qploidy citation info Materials: NEWS CRAN checks: Qploidy results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=Qploidy to link to this page.
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