context("makeGRangesFromGFF : Ensembl")
skip_if_not(hasInternet())
file <- file.path("cache", "ensembl.gtf")
test_that("GTF genes", {
object <- makeGRangesFromGFF(file = file, level = "genes")
expect_s4_class(object, "GRanges")
expect_identical(length(object), 60L)
expect_identical(names(object)[[1L]], "ENSG00000177757")
expect_identical(
object = lapply(mcols(object), class),
expected = list(
broadClass = Rle,
geneBiotype = Rle,
geneID = Rle,
geneName = Rle,
geneSource = Rle,
geneVersion = Rle,
source = Rle,
type = Rle
)
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGFF(file = file, level = "transcripts")
expect_s4_class(object, "GRanges")
expect_identical(length(object), 167L)
expect_identical(names(object)[[1L]], "ENST00000326734")
expect_identical(
object = lapply(mcols(object), class),
expected = list(
broadClass = Rle,
ccdsID = Rle,
geneBiotype = Rle,
geneID = Rle,
geneName = Rle,
geneSource = Rle,
geneVersion = Rle,
source = Rle,
tag = Rle,
transcriptBiotype = Rle,
transcriptID = Rle,
transcriptName = Rle,
transcriptSource = Rle,
transcriptSupportLevel = Rle,
transcriptVersion = Rle,
type = Rle
)
)
})
file <- file.path("cache", "ensembl.gff3")
test_that("GFF3 genes", {
object <- makeGRangesFromGFF(file = file, level = "genes")
expect_s4_class(object, "GRanges")
expect_identical(length(object), 53L)
expect_identical(names(object)[[1L]], "ENSG00000177757")
expect_identical(
object = lapply(mcols(object), class),
expected = list(
broadClass = Rle,
description = Rle,
geneBiotype = Rle,
geneID = Rle,
geneName = Rle,
logicName = Rle,
source = Rle,
type = Rle,
version = Rle
)
)
})
test_that("GFF3 transcripts", {
object <- makeGRangesFromGFF(file = file, level = "transcripts")
expect_s4_class(object, "GRanges")
expect_identical(length(object), 147L)
expect_identical(names(object)[[1L]], "ENST00000326734")
expect_identical(
object = lapply(mcols(object), class),
expected = list(
broadClass = Rle,
ccdsID = Rle,
description = Rle,
geneBiotype = Rle,
geneID = Rle,
geneName = Rle,
logicName = Rle,
source = Rle,
tag = Rle,
transcriptBiotype = Rle,
transcriptID = Rle,
transcriptName = Rle,
transcriptSupportLevel = Rle,
type = Rle,
version = Rle
)
)
})
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