inst/GSE47077/R/03.runC3co.R

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

##########################################################################
# Run c3co
##########################################################################
## Run 00.preprocessing.R, 01.CallGenotypes.R, 03.TumorBoost.R before running this file
library("c3co")
patient <- "RK29"
path <- "c3co.data"
dat <- readRDS(sprintf("%s/dat-%s.rds", path, patient))
lambda.grid <- c(2e-6,1e-5,2e-5) ## penalty
p.list <- 2:13 ## candidate number of subclones
parameters.grid <- list(lambda1=lambda.grid, lambda2=lambda.grid, nb.arch = p.list)
resC3co <- c3co(dat, parameters.grid = parameters.grid, pathSeg="segDat.rds", verbose=TRUE)