Nothing
setwd(file.path(getwd(), "testdata"))
context("Test that formatGTF() function works correctly")
test_that("formatGTF() generates the correct data structure", {
needColumns <-
c(
"chrom",
"start",
"end",
"width",
"strand",
"type",
"gene_name",
"transcript_id",
"exon_number"
)
pathToGTF <- "UCSCmm10.gtf"
gtf <- formatGTF(pathToGTF)
expect_equal(colnames(gtf), needColumns)
expect_is(gtf, "data.frame")
expect_equal(class(gtf$chrom), "character")
expect_equal(class(gtf$strand), "character")
expect_equal(class(gtf$exon_number), "numeric")
pathToGTF <- "ncbi38.gtf"
gtf <- formatGTF(pathToGTF)
expect_equal(colnames(gtf), needColumns)
expect_is(gtf, "data.frame")
expect_equal(class(gtf$chrom), "character")
expect_equal(class(gtf$strand), "character")
expect_equal(class(gtf$exon_number), "numeric")
pathToGTF <- "GRCm38.92.gtf"
gtf <- formatGTF(pathToGTF)
expect_equal(colnames(gtf), needColumns)
expect_is(gtf, "data.frame")
expect_equal(class(gtf$chrom), "character")
expect_equal(class(gtf$strand), "character")
expect_equal(class(gtf$exon_number), "numeric")
pathToGTF <- "gencodeVM16.gtf"
gtf <- formatGTF(pathToGTF)
expect_equal(colnames(gtf), needColumns)
expect_is(gtf, "data.frame")
expect_equal(class(gtf$chrom), "character")
expect_equal(class(gtf$strand), "character")
expect_equal(class(gtf$exon_number), "numeric")
# Check for chromosome MT
})
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