tests/testthat/test_c3co.R

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

library("c3co")

context("c3co test")

## randomness in getToyData sometimes gives results out of tolerance band
set.seed(7)

dataAnnotTP <- acnr::loadCnRegionData(dataSet = "GSE11976", tumorFraction = 1.0)
dataAnnotN <- acnr::loadCnRegionData(dataSet = "GSE11976", tumorFraction = 0.0)

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)
stopifnot(is.list(datSubClone), length(datSubClone) == K)

W <- rSparseWeightMatrix(nb.samp = n, nb.arch = K)
stopifnot(identical(dim(W), c(n, K)))

dat <- mixSubclones(subClones = datSubClone, W = W)
stopifnot(is.list(dat), length(dat) == nrow(W))

l1 <- 10^(-seq(from = 2, to = 8, by = 1L))
parameters.grid <- list(lambda = l1, nb.arch = 2:5)

test_that("c3co terminates on C1,C2", {
  res <- c3co(dat, parameters.grid = parameters.grid)
  stopifnot(inherits(res, "c3coFit"),
            is.list(res@segDat),
            all(c("Y1", "Y2", "Y") %in% names(res@segDat)))
              
  df <- createZdf(res, chromosomes = 1L, idxBest = 3L)
  stopifnot(is.data.frame(df))
            
  pvePlot(res)
  Zplot(df)
})

test_that("c3co terminates on TCN", {
  #expect_error(c3co(dat, parameters.grid = parameters.grid, stat = "TCN"))
   resC <- c3co(dat, parameters.grid = parameters.grid, stat = "TCN")
   expect_true(inherits(resC, "c3coFit"))
   # pvePlot(resC)
   
   df <- createZdf(resC, chromosomes = 1L, idxBest = 3L)
   expect_true(inherits(df, "data.frame"))
   # Zplot(df)
})