Qploidy: Estimation of Ploidy and Detection of Aneuploidy UsingGenotyping Data
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 |
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