Nothing
suppressWarnings(RNGversion(vstr = "3.5.3"))
test_that("BinarizeCounts works", {
set.seed(1)
# matrix
mat <- matrix(data = rbinom(n = 25, size = 5, prob = 0.2), nrow = 5)
bin_mat <- BinarizeCounts(object = mat)
# sparse matrix
mat_sparse <- as(object = mat, Class = "dgCMatrix")
bin_mat_sparse <- BinarizeCounts(object = mat_sparse)
expect_equal(
object = as.vector(bin_mat[1, ]), expected = c(0, 1, 0, 1, 1)
)
expect_equal(
object = as.vector(bin_mat_sparse[1, ]), expected = c(0, 1, 0, 1, 1)
)
})
test_that("DownsampleFeatures works", {
set.seed(1)
atac_ds <- DownsampleFeatures(object = atac_small, n = 5, verbose = FALSE)
expect_equal(
object = SeuratObject::VariableFeatures(object = atac_ds),
expected = c(
"chr1-1804025-1804468",
"chr1-2221250-2223390",
"chr1-6074646-6075340",
"chr1-8931013-8932013",
"chr1-1562519-1567986"
)
)
})
test_that("FindTopFeatures works", {
VariableFeatures(atac_small) <- NULL
atac_small <- FindTopFeatures(object = atac_small)
expect_equal(
object = head(SeuratObject::VariableFeatures(object = atac_small)),
expected = c("chr1-2157847-2188813",
"chr1-2471903-2481288",
"chr1-6843960-6846894",
"chr1-3815928-3820356",
"chr1-8935313-8940649",
"chr1-2515241-2519350")
)
})
test_that("FRiP works", {
atac_small <- FRiP(
object = atac_small,
assay = "peaks",
total.fragments = "fragments"
)
expect_equal(
object = as.vector(x = head(atac_small$FRiP)),
expected = c(
0.0069896591, 0.0086400864, 0.0102987567,
0.0093475841, 0.0081182600, 0.0001859341
),
tolerance = 1 / 100000
)
})
test_that("FeatureMatrix works", {
computed_fmat <- readRDS("../testdata/featurematrix.rds")
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
path = fpath,
cells = colnames(x = atac_small),
tolerance = 0.5,
verbose = FALSE
)
fm <- FeatureMatrix(
fragments = fragments,
features = granges(atac_small),
verbose = FALSE
)
expect_identical(object = fm, expected = computed_fmat)
})
test_that("NucleosomeSignal works", {
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
path = fpath,
cells = colnames(x = atac_small),
tolerance = 0.5,
verbose = FALSE
)
Fragments(object = atac_small) <- fragments
ns <- NucleosomeSignal(object = atac_small, verbose = FALSE)
expect_equal(
object = as.numeric(x = head(x = ns$nucleosome_signal)),
expected = c(NaN, NaN, 0.0, 2.5, NaN, NaN)
)
})
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