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)
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.