Package: scquantum

Title: Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing

Version: 1.0.0

Authors@R: c(

person(given = "Alexander",

family = "Davis",

role = c("aut", "cre"),

email = "alexlovesmolecules@gmail.com"),

person(given = "Taylor",

family = "Arnold",

role = "cph",

comment = "Author of segmentation function"),

person(given = "Veeranjaneyulu",

family = "Sadhanala",

role = "cph",

comment = "Author of segmentation function"),

person(given = "Ryan",

family = "Tibshirani",

role = "cph",

comment = "Author of segmentation function"))

Description: 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.

License: GPL (>= 2)

Encoding: UTF-8

LazyData: true

RoxygenNote: 7.1.2

Suggests:

testthat (>= 3.0.0)

Config/testthat/edition: 3