context("makeGRangesFromGFF : FlyBase")
skip_if_not(hasInternet())
file <- file.path("cache", "flybase.gtf")
test_that("GTF genes", {
expect_warning(
object = makeGRangesFromGFF(file = file, level = "genes"),
regexp = "Returning without broad class definitions."
)
suppressWarnings(
object <- makeGRangesFromGFF(file = file, level = "genes")
)
expect_s4_class(object, "GRanges")
expect_identical(length(object), 39L)
expect_identical(names(object)[[1L]], "FBgn0000022")
expect_identical(
object = lapply(mcols(object), class),
expected = list(
broadClass = Rle,
geneID = Rle,
geneName = Rle,
source = Rle,
type = Rle
)
)
})
test_that("GTF transcripts", {
expect_warning(
object = makeGRangesFromGFF(file = file, level = "transcripts"),
regexp = "Returning without broad class definitions."
)
suppressWarnings(
object <- makeGRangesFromGFF(file = file, level = "transcripts")
)
expect_s4_class(object, "GRanges")
expect_identical(length(object), 72L)
expect_identical(names(object)[[1L]], "FBtr0070000")
expect_identical(
object = lapply(mcols(object), class),
expected = list(
broadClass = Rle,
geneID = Rle,
geneName = Rle,
source = Rle,
transcriptID = Rle,
transcriptName = Rle,
type = Rle
)
)
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.