formula
.
Fitting uses previously calculated sizeFactors
(or normalizationFactors
)
and dispersion estimates.
nbinomLRT(object, full = design(object), reduced, betaPrior = FALSE, betaPriorVar, maxit = 100, useOptim = TRUE, quiet = FALSE, useQR = TRUE)
design(object)
.
alternatively, can be a matrixnbinomWaldTest
.results
function. The coefficients and standard errors are
reported on a log2 scale.
nbinomGLMTest
of the previous version of DESeq
and an alternative to the default nbinomWaldTest
.
DESeq
, nbinomWaldTest
dds <- makeExampleDESeqDataSet()
dds <- estimateSizeFactors(dds)
dds <- estimateDispersions(dds)
dds <- nbinomLRT(dds, reduced = ~ 1)
res <- results(dds)
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