Nothing
context("TransformCatalogSBS192")
test_that("Transformation of a SBS 192 catalog", {
skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
cat.t <- ReadCatalog("testdata/regress.cat.sbs.192.csv",
ref.genome = "GRCh37",
region = "transcript",
catalog.type = "counts")
x1 <-
expect_warning(TransformCatalog(cat.t, target.ref.genome = "GRCh37",
target.region = "exome",
target.catalog.type = "counts"))
x2 <-
expect_warning(TransformCatalog(x1, target.ref.genome = "GRCh37",
target.region = "transcript",
target.catalog.type = "counts"))
expect_equal(cat.t, x2)
cat.density <- TransformCatalog(cat.t, target.ref.genome = "GRCh37",
target.region = "transcript",
target.catalog.type = "density")
x3 <- TransformCatalog(x1, target.ref.genome = "GRCh37",
target.region = "exome",
target.catalog.type = "density")
null.cat.density <-cat.density
attr(null.cat.density, "region") <- NULL
null.x3 <- x3
attr(null.x3, "region") <- NULL
expect_equal(null.cat.density, null.x3)
rm(null.cat.density, null.x3)
genome.counts.signature <-
TransformCatalog(cat.t, target.ref.genome = "GRCh37",
target.region = "transcript",
target.catalog.type = "counts.signature")
expect_equal(colSums(genome.counts.signature),
rep(1, 4),
check.attributes = FALSE,
tolerance = .Machine$double.eps^0.5)
expect_error(TransformCatalog(genome.counts.signature,
target.ref.genome = "GRCh37",
target.region = "transcript",
target.catalog.type = "density"))
x4 <- TransformCatalog(genome.counts.signature,
target.ref.genome = "GRCh37",
target.region = "transcript",
target.catalog.type = "density.signature")
x5 <- TransformCatalog(cat.density,
target.ref.genome = "GRCh37",
target.region = "transcript",
target.catalog.type = "density.signature")
expect_equal(x4, x5)
})
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