tests/testthat/testPeaks.R

In jnkoberstein/DEScan: Differential Enrichment Scan

library(DEScan)
context("Peak Finding")

test_that("findPeaks is consistent with both bed and bam inputs", {
  test_bam <- system.file("extdata", "test.bam", package = "DEScan")

  bam_peaks <- findPeaks(test_bam, chr = 1, fraglen = 200, rlen = 100, min_win = 1,
                     max_win = 100, blocksize = 10000, zthresh = 5,
                     min_count = 0.1, grid = NA, filetype = "bam", save = F)

  expect_equal_to_reference(bam_peaks, file = "bam_peaks.rds")

  test_bed <- system.file("extdata", "test.bed", package = "DEScan")

  bed_peaks <- findPeaks(test_bed, chr = 1, fraglen = 200, rlen = 100, min_win = 1,
                     max_win = 100, blocksize = 10000, zthresh = 5,
                     min_count = 0.1, grid = NA, filetype = "bed", save = F)

  expect_equal_to_reference(bed_peaks, file = "bed_peaks.rds")

  expect_equal(bam_peaks, bed_peaks)
})