tests/testthat/test_addMLE.R

In nlhuong/ZeroInflatedDESeq2: Differential gene expression analysis based on the negative binomial distribution

set.seed(1)
dds <- makeExampleDESeqDataSet(n=200,m=12,betaSD=1)
dds$condition <- factor(rep(letters[1:3],each=4))
dds <- DESeq(dds)
ddsNP <- nbinomWaldTest(dds, betaPrior=FALSE)

res1 <- results(dds, contrast=c("condition","c","a"), addMLE=TRUE)
res2 <- results(ddsNP, contrast=c("condition","c","a"))
expect_equal(res1$lfcMLE, res2$log2FoldChange)

res1 <- results(dds, contrast=c("condition","a","b"), addMLE=TRUE)
res2 <- results(ddsNP, contrast=c("condition","a","b"))
expect_equal(res1$lfcMLE, res2$log2FoldChange)

res1 <- results(dds, contrast=c("condition","c","b"), addMLE=TRUE)
res2 <- results(ddsNP, contrast=c("condition","c","b"))
expect_equal(res1$lfcMLE, res2$log2FoldChange)

set.seed(1)
dds <- makeExampleDESeqDataSet(n=200,m=12,betaSD=1)
dds$group <- factor(rep(1:3,4))
design(dds) <- ~ group*condition
dds <- DESeq(dds)
ddsNP <- nbinomWaldTest(dds, betaPrior=FALSE)

res1 <- results(dds, name="group3.conditionB", addMLE=TRUE)
res2 <- results(ddsNP, name="group3.conditionB")
expect_equal(res1$lfcMLE, res2$log2FoldChange)