context("makeGRangesFromEnsDb : GRCh37 (hg19)")
pkg <- "EnsDb.Hsapiens.v75"
## Conditionally test if optional EnsDb.Hsapiens.v75 package is installed.
skip_if_not(pkg %in% rownames(installed.packages()))
test_that("Genes", {
x <- makeGRangesFromEnsDb(object = pkg, level = "genes")
expect_s4_class(x, "GRanges")
})
## Note that transcript versions aren't saved in this object.
test_that("Transcripts", {
x <- makeGRangesFromEnsDb(
object = pkg,
level = "transcripts",
ignoreTxVersion = TRUE
)
expect_s4_class(x, "GRanges")
})
context("makeGRangesFromEnsDb : AnnotationHub")
ah <- AnnotationHub::AnnotationHub()
edb <- ah[["AH73881"]]
test_that("Genes", {
x <- makeGRangesFromEnsDb(object = edb, level = "genes")
expect_s4_class(x, "GRanges")
})
test_that("Transcripts", {
x <- makeGRangesFromEnsDb(
object = edb,
level = "transcripts",
ignoreTxVersion = FALSE
)
expect_s4_class(x, "GRanges")
})
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