createReport_differential-methods — createReport_differential,DsATAC-method • ChrAccR

Create a report summarizing differential accessibility analysis

# S4 method for DsATAC
createReport_differential(.object, reportDir, chromVarObj = NULL)

Arguments

.object: DsATAC object
reportDir: directory in which the report will be created
chromVarObj: [optional] pre-computed result of a call to run_atac_chromvar(...)

Value

(invisible) muReportR::Report object containing the report

Author

Fabian Mueller

Examples

if (FALSE) {
dsa <- ChrAccRex::loadExample("dsAtac_ia_example")
reportDir <- file.path(".", "ChrAccR_reports")
setConfigElement("regionTypes", setdiff(getRegionTypes(dsa), c("promoters_gc_protein_coding", "t10k")))
setConfigElement("differentialColumns", c("stimulus", "cellType"))
# adjust for the donor annotation in the differential test
setConfigElement("differentialAdjColumns", c("donor"))
# create the report
createReport_differential(dsa, reportDir)
}