Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using
Genotyping 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 |
Documentation:
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