Nothing
suppressWarnings(suppressMessages(library(Rmmquant)))
suppressWarnings(suppressMessages(library(testthat)))
suppressWarnings(suppressMessages(library(GenomicRanges)))
context("Output tests")
dir <- system.file("extdata", package="Rmmquant", mustWork = TRUE)
test_that("Running default test", {
gtfFile <- file.path(dir, "test.gtf")
samFile <- file.path(dir, "test.sam")
se <- RmmquantRun(gtfFile, samFile)
table <- assays(se)[[1]]
stats <- colData(se)
expect_is(se, "SummarizedExperiment")
expect_is(table, "matrix")
expect_is(stats, "DataFrame")
})
test_that("Running empty output", {
gtfFile <- file.path(dir, "test.gtf")
samFile <- file.path(dir, "test.sam")
invisible(capture.output(se <- RmmquantRun(annotationFile=gtfFile,
readsFiles =samFile,
overlap =10000),
type="message"))
table <- assays(se)$counts
expect_is(table, "matrix")
expect_equal(dim(table), c(0, 1))
})
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