tests/testthat/test_get_counts.R

In chromVAR: Chromatin Variation Across Regions

context('getCounts')

# Read in data needed for tests ------------------------------------------------

test_rg <- system.file("extdata", "test_RG.bam", package = "chromVAR")
test_bam1 <- system.file("extdata", "test_single1.bam", package = "chromVAR")
test_bam2 <- system.file("extdata", "test_single2.bam", package = "chromVAR")
test_bam3 <- system.file("extdata", "test_single3.bam", package = "chromVAR")
peaks_file <- system.file("extdata", "test_bed.txt", package = "chromVAR")
test_peaks <- getPeaks(peaks_file, sort = TRUE)
test_bed <- system.file("extdata", "test_reads.bed", package = "chromVAR")

# Test fragment counts with RG ___________--------------------------------------

test_that("can count fragments using RG tags", {
  counts <- getCounts(test_rg, test_peaks, by_rg = TRUE, paired = TRUE)
  expect_is(counts, "RangedSummarizedExperiment")
  expect_equal(assays(counts)$counts[11,2][[1]],1)
  expect_equal(sum(assays(counts)$counts),1)
  expect_equal(sum(colData(counts)$depth), 27)
})


# Test fragment counts with multiple bam --------------------------------------

test_that("can count fragments with multiple bams", {
  counts <- getCounts(c(test_bam1, test_bam2, test_bam3), test_peaks, 
                      by_rg = FALSE, paired = TRUE)
  expect_is(counts, "RangedSummarizedExperiment")
  expect_equal(assays(counts)$counts[11,3][[1]],1)
  expect_equal(sum(assays(counts)$counts),1)
  expect_equal(colData(counts)$depth, c(26,14,2))
})



# Test fragment counts with bed file -------------------------------------------

test_that("can count fragments with bed file", {
  counts <- getCounts(test_bed, test_peaks, by_rg = FALSE, paired = FALSE, 
                      format = "bed")
  expect_is(counts, "RangedSummarizedExperiment")
  expect_equal(assays(counts)$counts[2,1][[1]], 2)
  expect_equal(assays(counts)$counts[5,1][[1]], 1)
  expect_equal(colData(counts)$depth, 4)
  expect_equal(getTotalFragments(counts),3)
})