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context("test-bin_mutation_density")
# Read grl
grl <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
package = "MutationalPatterns"
))
## Load the corresponding reference genome.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)
## Determine region density
output <- bin_mutation_density(grl, ref_genome, nrbins = 3)
# Use manual cutoffs
output_man <- bin_mutation_density(grl, ref_genome, man_dens_cutoffs = c(0, 2e-08, 1))
# Tests
test_that("Output has correct class", {
expect_true(inherits(output, "CompressedGRangesList"))
expect_true(inherits(output_man, "CompressedGRangesList"))
})
test_that("Output has correct dimensions", {
expect_equal(length(output), 3)
expect_equal(length(output_man), 2)
expect_equal(as.vector(S4Vectors::elementNROWS(output)), c(30, 11, 2))
expect_equal(as.vector(S4Vectors::elementNROWS(output_man)), c(25, 4))
})
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