createReport_exploratory-methods — createReport_exploratory,DsATAC-method • ChrAccR

Create a report summarizing exploratory analyses of an accessibility dataset

# S4 method for 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

Fabian Mueller

Examples

if (FALSE) {
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)
}