tests/testthat/test_buildSubclones.R

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

library("c3co")

context("Construction of subclones")

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

len <- 500 * 10  ## Number of loci
K <- 2L          ## Number of subclones

bkps <- list(
  c(100, 250) * 10,
  c(150, 400) * 10
)

regions <- list(
  c("(0,3)", "(0,2)", "(1,2)"),
  c("(1,1)", "(0,1)", "(1,1)")
)

for (what in c("real", "simulated")) {
    if (what=="real") {
        datSubClone <- buildSubclones(len = len,
                                      nbClones = K,
                                      bkps = bkps,
                                      regions = regions,
                                      dataAnnotTP = dataAnnotTP,
                                      dataAnnotN = dataAnnotN)
    } else if (what=="simulated") {
        datSubClone <- buildSubclones(len = len,
                                      nbClones = K,
                                      bkps = bkps,
                                      regions = regions)
    }
    
    test_that("built subclones have the expected size and column names", {
        expect_length(datSubClone, K)
        enames <- c("ct", "baft", "genotype", "region","cn", "bafn", "pos")
        for (ii in seq_along(datSubClone)) {
            sc <- datSubClone[[ii]]
            expect_equal(nrow(sc), len)
            
            nms <- names(sc)
            expect_equal(ncol(sc), length(enames))
            for (enm in enames) {
                expect_true(enm %in% nms)
            }
        }
    })
    
    test_that("built subclones have identical genotypes", {
        geno <- datSubClone[[1]]$genotype
        for (ii in seq_along(datSubClone)) {
            gg <- datSubClone[[ii]]$genotype
            expect_identical(gg, geno)
        }
    })
}