getDESeq2Dataset-methods

Retrieve a differential expression dataset computed with DESeq2

# S4 method for DsATAC
getDESeq2Dataset(.object, regionType, designCols = NULL, compTab = NULL, ...)

Arguments

.object

DsATAC object

regionType

character string specifying the region type

designCols

column names in the sample annotation potentially used to create the design matrix

compTab

if design columns are not specified, you can specify a comparison table directly. These comparison tables can be obtained by getComparisonTable(...)

...

parameters passed on to DESeq2::DESeq

Value

DESeqDataSet as returned by DESeq2::DESeq

Author

Fabian Mueller

Examples

if (FALSE) {
dsa <- ChrAccRex::loadExample("dsAtac_ia_example")
dds <- getDESeq2Dataset(dsa, "IA_prog_peaks", designCols=c("donor", "stimulus", "cellType"))
dds
}