## Parameters
exppath <-  system.file("extdata", "exptab.csv", package="tepr")
transpath <- system.file("extdata", "cugusi_6.tsv", package="tepr")
expthres <- 0.1

## Calculating necessary results
expdf <- read.csv(exppath)
transdf <- read.delim(transpath, header = FALSE)
avfilt <- averageandfilterexprs(expdf, transdf, expthres,
        showtime = FALSE, verbose = FALSE)
rescountna <- countna(avfilt, expdf, nbcpu = 1, verbose = FALSE)
ecdf <- genesECDF(avfilt, expdf, verbose = FALSE)
resecdf <- ecdf[[1]]
nbwindows <- ecdf[[2]]
resmeandiff <- meandifference(resecdf, expdf, nbwindows,
    verbose = FALSE)
bytranslistmean <- split(resmeandiff, factor(resmeandiff$transcript))
resknee <- kneeid(bytranslistmean, expdf, verbose = FALSE)
resauc <- allauc(bytranslistmean, expdf, nbwindows, verbose = FALSE)
resatt <- attenuation(resauc, resknee, rescountna, bytranslistmean, expdf,
        resmeandiff, verbose = FALSE)

## ---- Comparing to expected object ---- ##
expectedobj <- readRDS(system.file("extdata", "universegroup.rds",
    package="tepr"))
resug <- universegroup(resatt, expdf, verbose = FALSE)
test_that("universegroup works properly", {

    ## Darwin indicates a macos. Because of floating system, object is
    ## equal but not identical on this OS.
    if (!isTRUE(all.equal(Sys.info()[['sysname']], "Darwin"))) {
        expect_identical(resug, expectedobj)
    } else {
        expect_equal(resug, expectedobj)
    }
})