library(SummarizedExperiment)

library(biotmleData)

data(illuminaData)

## SETUP TESTS ################################################################

set.seed(6423709)

n <- 50

g <- 2500

cases_pois <- 50

controls_pois <- 10

ngs_cases <- as.data.frame(matrix(replicate(n, rpois(g, cases_pois)), g))

ngs_controls <- as.data.frame(matrix(replicate(n, rpois(g, controls_pois)), g))

ngs_data <- as.data.frame(cbind(ngs_cases, ngs_controls))

exp_var <- c(rep(1, n), rep(0, n))

batch <- rep(1:2, n)

covar <- rep(1, n * 2)

design <- as.data.frame(cbind(exp_var, batch, covar))

se <- SummarizedExperiment(

  assays = list(counts = DataFrame(ngs_data)),

  colData = DataFrame(design)

)

call <- "testing" # dumb workaround to failure of match.call() for now...

class(call) <- "call" # force class to be what biotmle expects...

biotmle <- .biotmle(

  SummarizedExperiment(

    assays = list(expMeasures = assay(se)),

    rowData = rowData(se),

    colData = colData(se)

  ),

  call = call,

  tmleOut = as.data.frame(matrix(NA, 10, 10)),

  topTable = as.data.frame(matrix(NA, 10, 10))

)

voom_out <- rnaseq_ic(biotmle)

## BEGIN TESTS ################################################################

test_that("Object returned by RNA-seq tools matches output of voom", {

  expect_is(voom_out, "EList")

})

test_that("Object returned by RNA-seq tools is of correct dimensionality", {

  expect_equal(dim(voom_out), c(g, 2 * n))

})