tests/testthat/test-runSegmentation.R

In navinlabcode/copykit: CopyKit

# setup
copykit_obj_50kb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "55kb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)
copykit_obj_50kb <- runVst(copykit_obj_50kb)

copykit_obj_100kb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "110kb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)

copykit_obj_175kb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "195kb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)

copykit_obj_200kb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "220kb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)

copykit_obj_250kb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "280kb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)

copykit_obj_500kb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "500kb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)

copykit_obj_1Mb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "1Mb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)

copykit_obj_2Mb <- mock_bincounts(
    ncells = 10,
    ncells_diploid = 5,
    position_gain = 1:50,
    position_del = 200:250,
    resolution = "2.8Mb",
    run_segmentation = FALSE,
    run_lognorm = FALSE
)


# test
test_that("Testing CopyKit runSegmentation for different resolutions: ", {
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_50kb), "CopyKit")
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_100kb), "CopyKit")
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_175kb), "CopyKit")
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_200kb), "CopyKit")
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_250kb), "CopyKit")
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_500kb), "CopyKit")
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_1Mb), "CopyKit")
    expect_s4_class(copykit_obj <- runSegmentation(copykit_obj_2Mb), "CopyKit")
})