scquantum

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.