Package: scquantum 1.0.0

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.

Authors:Alexander Davis [aut, cre], Taylor Arnold [cph], Veeranjaneyulu Sadhanala [cph], Ryan Tibshirani [cph]

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Last updated 2 years agofrom:b6fcd39eef. Checks:OK: 9. Indexed: yes.

Exports:ecf.global.maxexpected.peak.heightsgatirises.pluspurplel2e.normal.sdploidy.inferenceprof2invalsquantum.sdseg2invalssegment.summarizetf.dptimeseries.iodweighted.ecf

Dependencies: