createReport_exploratory-DsATAC-method: createReport_exploratory-methods

In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

createReport_exploratory-methods

Description

Create a report summarizing exploratory analyses of an accessibility dataset

Usage

## S4 method for signature 'DsATAC'
createReport_exploratory(
  .object,
  reportDir,
  chromVarObj = NULL,
  itLsiObj = NULL,
  geneActSe = 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(...)
itLsiObj	[for single-cell only; optional] pre-computed result of a call to iterativeLSI(.object, ...)
geneActSe	[for single-cell only; optional] pre-computed result of a call to getCiceroGeneActivities(.object, ...)

Value

(invisible) muReportR::Report object containing the report

Author(s)

Fabian Mueller

Examples

## Not run: 
dsa <- ChrAccRex::loadExample("dsAtac_ia_example")
dsa_qnorm <- transformCounts(dsa, method="quantile")
setConfigElement("annotationColumns", c("cellType", "donor", "stimulus"))
setConfigElement("regionTypes", setdiff(getRegionTypes(dsa), c("promoters_gc_protein_coding", "t10k")))
reportDir <- file.path(".", "ChrAccR_reports")
createReport_exploratory(dsa_qnorm, reportDir)

## End(Not run)

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