In pneuvial/c3co: Cancer Cell Clonality using Copy-Number

This vignette aims to help users to run c3co on segmented data.

This example is based on segmented data from GSE47077 data sets. This data set is in the c3co.data package. It is also possible to use c3co algorithm from an RDS file containing segmentation.

Note that the file or the data must be a list with elements as follows

data("segDat", package = "c3co.data")
names(segDat)

str(segDat)

library("c3co")
lambda.grid <- 10^-(3:5) ## penalty
K.list <- 2:5 ## candidate number of subclones
parameters.grid <- list(lambda = lambda.grid, nb.arch = K.list)
resc3co <- c3co(NULL, segDat = segDat, parameters.grid = parameters.grid)