createReport_differential-DsATAC-method: createReport_differential-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

createReport_differential-methods

Description

Create a report summarizing differential accessibility analysis

Usage

## S4 method for signature 'DsATAC'
createReport_differential(.object, reportDir)

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(s)

Fabian Mueller

Examples

## Not run: 
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)

## End(Not run)

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