Nothing
test_that("invalid column names throw error", {
x <- tibble::tribble(
~pork, ~pie, ~hat,
"chr1", 1, 50
)
expect_error(check_interval(x), "expected 3 required names, missing: chrom, start, and end")
# missing 1 only
x <- tibble::tribble(
~chrom, ~start, ~oops,
"chr1", 1, 50
)
expect_error(check_interval(x), "expected 3 required names, missing: end")
})
test_that("invalid column names throw error", {
genome <- tibble::tribble(
~foo, ~bar,
"chr1", 1e4
)
expect_error(check_genome(genome), "expected 2 required names, missing: chrom and size")
})
test_that("duplicate chromosomes refs throw error", {
genome <- tibble::tribble(
~chrom, ~size,
"chr1", 1e4,
"chr1", 1e4
)
expect_error(check_genome(genome), "duplicate chroms in genome: chr1")
})
test_that("gr_to_bed coerces GRanges objects", {
skip_if_not_installed("GenomicRanges")
suppressMessages(require(GenomicRanges))
gr <- GRanges(
seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges = IRanges(1:10, end = 7:16, names = head(letters, 10)),
strand = Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2))
)
res <- gr_to_bed(gr)
expect_silent(check_interval(res))
expect_true("tbl_df" %in% class(res))
})
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