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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 |
| Reference manual: | Qploidy.pdf |
| Vignettes: |
Qploidy (source, R code) |
| Package source: | Qploidy_1.0.1.tar.gz |
| Windows binaries: | r-devel: Qploidy_1.0.1.zip, r-release: Qploidy_1.0.1.zip, r-oldrel: Qploidy_1.0.1.zip |
| macOS binaries: | r-release (arm64): Qploidy_1.0.1.tgz, r-oldrel (arm64): Qploidy_1.0.1.tgz, r-release (x86_64): Qploidy_1.0.1.tgz, r-oldrel (x86_64): Qploidy_1.0.1.tgz |
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These binaries (installable software) and packages are in development.
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