context("Creation of realistic synthetic copy number profiles by 'getCopyNumberDataByResampling'")
tf <- 1
affyDat <- loadCnRegionData(dataSet="GSE29172", tumorFraction=tf)
sim <- getCopyNumberDataByResampling(len=1e4, nBkp=2, minLength=100, regData=affyDat)
Y <- sim$profile
bkp <- sim$bkp
regions <- sim$regions
test_that("Output cellularity is consistent with input", {
cl <- unique(Y$cellularity)
expect_identical(cl, tf)
})
test_that("Number of breakpoints + 1 is number of regions", {
nBkp <- length(bkp)
nReg <- length(regions)
expect_equal(nBkp+1, nReg)
regs <- as.factor(Y[["region"]])
nBkp2 <- sum(diff(as.numeric(regs))!=0)
expect_equal(nBkp, nBkp2)
})
test_that("Output breakpoints are identical to input when provided", {
sim2 <- getCopyNumberDataByResampling(1e4, bkp=bkp, regData=affyDat)
expect_identical(sim2$bkp, bkp)
})
test_that("Output regions are identical to input when provided", {
sim3 <- getCopyNumberDataByResampling(1e4, regions=regions, regData=affyDat)
expect_identical(sim3$regions, regions)
})
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