### Package to load
library(c3co)
library(FLLat)
library(parallel)
library(R.utils)
library(acnr)
## Number of subclones
p.list <- 2:15
## Type of simulations
framework <- "realistic"
## Force simulation and weights
forceM <- forceSim <- FALSE
## Number of simulated data sets
Bmax <- 100
### Parameters
len <- 800*3
## 3 is to obtain around 8000 point for heterozygous
nBkp <- 10
message("Path to save subclones : simArchData")
pathSimArch <- Arguments$getWritablePath("simArchData")
filename <- file.path(pathSimArch, "subClones.rds")
nbClones <- 5
####################################################################
## parameters of subclones and samples
####################################################################
set.seed(10)
if (!file.exists(filename)){
message("subClones.rds doesn't exist in simArchData directory")
subClones <- createSubclones(nbClones, len, nBkp)
saveRDS(subClones, filename)
}else {
subClones <- readRDS(filename)
message("subClones.rds has been loaded")
}
### Simulate Samples
message("Simulations of subclones")
n <- 30
forcec3co <- TRUE
pathWeight <- Arguments$getWritablePath(sprintf("weightData"))
B <- 1:Bmax
for (bb in B) {
filename <- sprintf("weight,n=%s,b=%s.rds", n,bb)
runWeights <- (forceM || !file.exists(file.path(pathWeight, filename)))
if (runWeights) {
message(sprintf("Create and save weight matrix for sample %s", bb))
M <- getWeightMatrix(70,20, nbClones, n)
saveRDS(M,file = file.path(pathWeight, filename))
}else{
message(sprintf("Load weight matrix for sample %s", bb))
M <- readRDS(file.path(pathWeight, filename))
}
pathSim <- Arguments$getWritablePath(sprintf("simData"))
fileSim <- sprintf("%s/dat_B=%s.rds",pathSim,bb)
runSim <- (forceSim || !file.exists(fileSim))
if (runSim) {
### simulations of samples
message(sprintf("Create and save DNA copy number profile for sample %s", bb))
dat <- apply(M, 1, mixSubclones, subClones = subClones, fracN = NULL)
saveRDS(dat, fileSim)
}else{
message(sprintf("Load DNA copy number profile for sample %s", bb))
dat <- readRDS(sprintf("%s/dat_B=%s.rds",pathSim,bb))
}
}
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