tests/testthat/test_WW.R

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

library("c3co")

set.seed(90)

dataAnnotTP <- acnr::loadCnRegionData(dataSet="GSE11976", tumorFrac=1)
dataAnnotN <- acnr::loadCnRegionData(dataSet="GSE11976", tumorFrac=0)

len <- 500*10   ## Number of loci
K <- 3L         ## Number of subclones
n <- 15L        ## Number of samples

bkps <- list(c(100, 250)*10, c(150, 400)*10, c(150, 400)*10)
regions <- list(c("(0,3)", "(0,2)", "(1,2)"),
                c("(1,1)", "(0,1)", "(1,1)"), 
                c("(0,2)", "(0,1)", "(1,1)"))

datSubClone <- buildSubclones(len=len, nbClones=K, bkps=bkps, regions=regions,
                              dataAnnotTP=dataAnnotTP, dataAnnotN=dataAnnotN)
W <- rSparseWeightMatrix(nb.samp=n, nb.arch=K, sparse.coeff=0.7)
dat <- mixSubclones(subClones=datSubClone, W=W)
seg <- segmentData(dat)

test_that("fitC3co terminates on C1C2", {
  lambda <- 0.01
  Y <- list(Y1=t(seg$Y1), Y2=t(seg$Y2))
  Z0t <- initializeZt(Y$Y1, Y$Y2, K=K)
  Zt <- Z0t[c("Z1", "Z2")]
  res <- positiveFusedLasso(Y, Zt, lambda=rep(lambda, times=2L), verbose=TRUE)
})