tests/testthat/test-edger_ftest_contrasts.R

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

context("edger_ftest_contrasts")

test_that("edger ftest contrasts", {

  #default
  res <- edger_ftest_contrasts(dge, grp=grp, contrast.v = contr.v)
  expect_equal(rownames(res$mtt)[1:4], paste0("gene", c(3,1,2,18)))

  #LRT
  res <- edger_ftest_contrasts(dge, grp=grp, contrast.v = contr.v, test="LRT")
  expect_equal(rownames(res$mtt)[1:4], paste0("gene", c(3,1,2, 18)))

  # design
  res <- edger_ftest_contrasts(dge, grp=grp, contrast.v = contr.v, design = design)
  expect_equal(rownames(res$mtt)[1:4], paste0("gene", c(3,1,2, 22)))

  # weights
  dge1 <- dge
  dge1$weights <- el$weights
  res <- edger_ftest_contrasts(dge1, grp=grp, contrast.v = contr.v, test="WeightedFT")
  expect_equal(rownames(res$mtt)[1:4], paste0("gene", c(3,1,2,18)))
})