getDESeq2Dataset-DsATAC-method: getDESeq2Dataset-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

getDESeq2Dataset-methods

Description

Retrieve a differential expression dataset computed with DESeq2

Usage

## S4 method for signature '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(s)

Fabian Mueller

Examples

## Not run: 
dsa <- ChrAccRex::loadExample("dsAtac_ia_example")
dds <- getDESeq2Dataset(dsa, "IA_prog_peaks", designCols=c("donor", "stimulus", "cellType"))
dds

## End(Not run)

GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.