Wrapper to run DESeq2: create the DESeqDataSet, normalize data, estimate dispersions, statistical testing...
run.DESeq2(counts, target, varInt, batch = NULL, locfunc = "median",
fitType = "parametric", pAdjustMethod = "BH", cooksCutoff = TRUE,
independentFiltering = TRUE, alpha = 0.05, ...)matrix of raw counts
target data.frame of the project
name of the factor of interest (biological condition)
batch effect to take into account (NULL by default)
"median" (default) or "shorth" to estimate the size factors
mean-variance relationship: "parametric" (default) or "local"
p-value adjustment method: "BH" (default) or "BY" for instance
outliers detection threshold (TRUE to let DESeq2 choosing it or FALSE to disable the outliers detection)
TRUE or FALSE to perform the independent filtering or not
significance threshold to apply to the adjusted p-values
optional arguments to be passed to nbinomWaldTest()
A list containing the dds object (DESeqDataSet class), the results objects (DESeqResults class) and the vector of size factors