tests/testthat/test_BSmeth2Probe.R

In BIMSBbioinfo/deconvR: Simulation and Deconvolution of Omic Profiles

library(deconvR)

test_that("BSmeth2Probe", {
  load(system.file("extdata", "WGBS_GRanges.rda",
    package = "deconvR"
  ))
  data("IlluminaMethEpicB5ProbeIDs")
  IlluminaMethEpicB5ProbeIDs_df <-
    GenomicRanges::as.data.frame(IlluminaMethEpicB5ProbeIDs)

  results <- BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = WGBS_GRanges
  )

  expect_equal(class(results), "data.frame")
  expect_equal(NCOL(results), 1 +
    length(colnames(GenomicRanges::mcols(WGBS_GRanges))))
  expect_equal(colnames(results), c(
    "IDs",
    colnames(GenomicRanges::mcols(WGBS_GRanges))
  ))
  expect_equal(class(results[[2]]), "numeric")
  expect_equal(class(results[[1]]), "character")
  expect_gt(NROW(results), 0)
  expect_true(all(results$methylation >= 0))
  expect_true(all(results$methylation <= 1))
  expect_true(all(is.element(results$ID, IlluminaMethEpicB5ProbeIDs$ID)))
  expect_lt(NROW(results), NROW(IlluminaMethEpicB5ProbeIDs))
  expect_lt(NROW(results), NROW(WGBS_GRanges))

  expect_error(NROW(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs[0],
    WGBS_data = WGBS_GRanges
  )))
  expect_error(NROW(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = WGBS_GRanges[0]
  )))

  expect_lt(NROW(results), NROW(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = WGBS_GRanges,
    cutoff = 100
  )))
  expect_gt(NROW(results), NROW(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = WGBS_GRanges,
    cutoff = 0
  )))
  expect_equal(NROW(results), NROW(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = WGBS_GRanges,
    multipleMapping = TRUE
  )))
  expect_gt(NROW(results), NROW(BSmeth2Probe(
    probe_id_locations =
      IlluminaMethEpicB5ProbeIDs[1:NROW(IlluminaMethEpicB5ProbeIDs) / 2],
    WGBS_data = WGBS_GRanges
  )))
  expect_gt(NROW(results), NROW(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data =
      WGBS_GRanges[1:NROW(WGBS_GRanges) / 2]
  )))

  expect_equal(results, BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs_df,
    WGBS_data = WGBS_GRanges
  ))
  expect_equal(
    colnames(BSmeth2Probe(
      probe_id_locations = IlluminaMethEpicB5ProbeIDs,
      WGBS_data = methylKit::methRead(list(
        system.file("extdata", "test1.myCpG.txt",
          package = "methylKit"
        ),
        system.file("extdata", "test2.myCpG.txt",
          package = "methylKit"
        )
      ),
      sample.id = list("test1", "test2"), assembly = "hg18",
      treatment = c(1, 1), context = "CpG"
      )
    )),
    c("IDs", methylKit::getSampleID(methylKit::methRead(list(
      system.file("extdata", "test1.myCpG.txt",
        package = "methylKit"
      ),
      system.file("extdata", "test2.myCpG.txt",
        package = "methylKit"
      )
    ),
    sample.id = list("test1", "test2"), assembly = "hg18",
    treatment = c(1, 1), context = "CpG"
    )))
  )
  expect_equal(
    colnames(BSmeth2Probe(
      probe_id_locations = IlluminaMethEpicB5ProbeIDs,
      WGBS_data = methylKit::methRead(list(
        system.file("extdata", "test1.myCpG.txt",
          package = "methylKit"
        ),
        system.file("extdata", "test2.myCpG.txt",
          package = "methylKit"
        )
      ),
      sample.id = list("test1", "test2"), assembly = "hg18",
      treatment = c(1, 1), context = "CpG"
      )
    )),
    colnames(BSmeth2Probe(
      cutoff = 100, probe_id_locations = IlluminaMethEpicB5ProbeIDs,
      WGBS_data = methylKit::methRead(list(
        system.file("extdata", "test1.myCpG.txt",
          package = "methylKit"
        ),
        system.file("extdata", "test2.myCpG.txt",
          package = "methylKit"
        )
      ),
      sample.id = list("test1", "test2"), assembly = "hg18",
      treatment = c(1, 1), context = "CpG"
      )
    ))
  )

  simulatedData <- methylKit::dataSim(
    replicates = 4, sites = 200000,
    treatment = c(1, 1, 0, 0),
    percentage = 10, effect = 25
  )
  expect_gte(NROW(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs_df,
    WGBS_data = simulatedData
  )), 0)
  expect_equal(
    NCOL(BSmeth2Probe(
      probe_id_locations = IlluminaMethEpicB5ProbeIDs_df,
      WGBS_data = simulatedData
    )),
    length(methylKit::getSampleID(simulatedData)) + 1
  )


  expect_error(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = WGBS_GRanges, cutoff = -1
  ))
  expect_error(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = IlluminaMethEpicB5ProbeIDs
  ))
  expect_error(BSmeth2Probe(
    probe_id_locations = WGBS_GRanges,
    WGBS_data = WGBS_GRanges
  ))
  expect_error(BSmeth2Probe(
    probe_id_locations = NULL,
    WGBS_data = WGBS_GRanges
  ))
  expect_error(BSmeth2Probe(
    probe_id_locations = IlluminaMethEpicB5ProbeIDs,
    WGBS_data = NULL
  ))
})