scquantum: Estimate Ploidy and Absolute Copy Number from Single Cell
Sequencing
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 |
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