tests/testthat/test-localPeaks.R

In sjessa/chromswitch: An R package to detect chromatin state switches from epigenomic data

context("LocalPeaks class")

test_that("LocalPeaks access works", {

    pks_in_region <- list(A = GRanges(seqnames = rep("chr1", 2),
                                      ranges = IRanges(start = c(100, 150),
                                                       end = c(200, 250))),
                          B = GRanges(seqnames = rep("chr1", 2),
                                      ranges = IRanges(start = c(100, 150),
                                                       end = c(200, 250))))

    region <- GRanges(seqnames = "chr1",
                      ranges = IRanges(start = 100, end = 300))

    lpk <- LocalPeaks(region, pks_in_region, c("A", "B"))

    expect_equal(region(lpk), region)
    expect_equal(samples(lpk), c("A", "B"))
    expect_equal(peaks(lpk), pks_in_region)

})


test_that("isEmpty finds empty LocalPeaks", {

    region <- GRanges(seqnames = "chr1",
                      ranges = IRanges(start = 100, end = 300))
    pks    <- GRanges(seqnames = c(), ranges = IRanges(start = c(), end = c()))
    pks_in_region <- list(A = GRanges(seqnames = rep("chr1", 2),
                                      ranges = IRanges(start = c(100, 150),
                                                       end = c(200, 250))),
                          B = GRanges(seqnames = rep("chr1", 2),
                                      ranges = IRanges(start = c(100, 150),
                                                       end = c(200, 250))))
    expect_equal(isEmpty(LocalPeaks(region,
                                     list(A = pks, B = pks),
                                     c("A", "B"))),
                 TRUE)

    expect_equal(isEmpty(LocalPeaks(region,
                                     list(A = pks_in_region, B = pks_in_region),
                                     c("A", "B"))),
                 FALSE)

})


test_that("LocalPeaks construction", {

    # Factor samples are ok
    x <- c("a", "b", "c")
    f <- as.factor(x)
    out <- LocalPeaks(region = GRanges(seqnames = "chr1:100-200"),
               peaks = H3K4me3,
               samples = x)

    expect_equal(LocalPeaks(region = GRanges(
                            seqnames = "chr1:100-200"),
                            peaks = H3K4me3,
                            samples = f), out)

})