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Given bincount data from single-cell copy number profiling (segmented or unsegmented), estimates ploidy, and uses the ploidy estimate to scale the data to absolute copy numbers. Uses the modular quantogram proposed by Kendall (1986) <doi:10.1002/0471667196.ess2129.pub2>, modified by weighting segments according to confidence, and quantifying confidence in the estimate using a theoretical quantogram. Includes optional fused-lasso segmentation with the algorithm in Johnson (2013) <doi:10.1080/10618600.2012.681238>, using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.
| Version: | 1.0.0 |
| Suggests: | testthat (≥ 3.0.0) |
| Published: | 2022-03-23 |
| DOI: | 10.32614/CRAN.package.scquantum |
| Author: | Alexander Davis [aut, cre], Taylor Arnold [cph] (Author of segmentation function), Veeranjaneyulu Sadhanala [cph] (Author of segmentation function), Ryan Tibshirani [cph] (Author of segmentation function) |
| Maintainer: | Alexander Davis <alexlovesmolecules at gmail.com> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | yes |
| Materials: | README |
| CRAN checks: | scquantum results |
| Reference manual: | scquantum.pdf |
| Package source: | scquantum_1.0.0.tar.gz |
| Windows binaries: | r-devel: scquantum_1.0.0.zip, r-release: scquantum_1.0.0.zip, r-oldrel: scquantum_1.0.0.zip |
| macOS binaries: | r-release (arm64): scquantum_1.0.0.tgz, r-oldrel (arm64): scquantum_1.0.0.tgz, r-release (x86_64): scquantum_1.0.0.tgz, r-oldrel (x86_64): scquantum_1.0.0.tgz |
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