context("test-classifiers.R")
test_that("da_tss returns all valid hits", {
result <- da_tss(tss, genes)
## Count hits.
expect_equal(length(result), length(idx_da_tss))
## Check distances.
expect_equal(mcols(result)$distance, dist_da_tss)
## Check from-to (# nolint) mapping.
expected <- Hits(from = idx_da_tss,
to = rep(1:2, each = 3),
nLnode = length(tss),
nRnode = length(genes),
distance = dist_da_tss)
expect_equal(expected, result)
})
test_that("da_tss validates that genes do not overlap", {
expect_error(da_tss(tss, genes_overlapping), "overlap")
})
test_that("da_tss validates min parameter", {
expect_error(da_tss(tss, genes, min = 400, max = 300), "min")
})
test_that("ua_rna returns all valid hits", {
result <- ua_rna(tss, genes)
## count hits.
expect_equal(length(result), length(idx_ua_rna))
## Check distances.
expect_equal(mcols(result)$distance, dist_ua_rna)
## Check from-to (# nolint) mapping.
expected <- Hits(from = idx_ua_rna,
to = 1:2,
nLnode = length(tss),
nRnode = length(genes),
distance = dist_ua_rna)
expect_equal(expected, result)
})
test_that("enhancer validates tre strandedness", {
BiocGenerics::strand(tre[2]) <- "-"
expect_error(enhancer(tre, genes), "strand")
BiocGenerics::strand(tre[2]) <- "+"
expect_error(enhancer(tre, genes), "strand")
})
test_that("enhancer subsets valid GRanges", {
result <- enhancer(tre, genes)
expected <- tre[idx_enhancer]
expect_equal(expected, result)
})
test_that("annotate classifies all features", {
result <- annotate(tss, genes)
is_da_tss <- mcols(result)$class %in% "daTSS"
expect_equal(sum(is_da_tss), length(idx_da_tss))
expect_equal(which(is_da_tss), idx_da_tss)
})
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