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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.
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Package details |
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| 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@gmail.com> |
| License | GPL (>= 2) |
| Version | 1.0.0 |
| Package repository | View on CRAN |
| Installation |
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