tests/testthat/test_DESeq.R

In DESeq2: Differential gene expression analysis based on the negative binomial distribution

context("DESeq")
test_that("DESeq() gives correct errors", {
  dds <- makeExampleDESeqDataSet(n=100, m=8)
  expect_error(DESeq(dds, test="LRT"))
  expect_error(DESeq(dds, test="Wald", full=~condition, reduced=~1))
  expect_error(DESeq(dds, full=~1))
  
  m <- model.matrix(~ condition, colData(dds))
  expect_error(DESeq(dds, test="LRT", full=m, reduced=~1))
  expect_error(DESeq(dds, test="LRT", full=m, reduced=m))
  expect_error(DESeq(dds, full=m, betaPrior=TRUE))
  
  design(dds) <- ~ 0 + condition
  expect_error(DESeq(dds, betaPrior=TRUE))
  
  dds <- makeExampleDESeqDataSet(n=100)
  dds$condition <- factor(rep(c("A","B","C"),each=4))
  dds <- dds[,1:8]
  expect_error(DESeq(dds))
})