Run contaminant RNA correction on a Seurat object

Usage

RunContamCorrection(
  object,
  method,
  decontXArgs = list(),
  scCDCArgs = list(Detection = list(), Quantification = list(), Correction = list()),
  keep_contam_assay = FALSE,
  log = NULL
)

Arguments

object: Seurat object
method: Method to use for contaminant RNA correction. Must be one of "decontx" (using decontX function from the celda package) and "sccdc" (using scCDC package), case-insensitively.
decontXArgs: Arguments to pass to decontX function from the celda package. See ?celda::decontX for details.
scCDCArgs: Arguments to pass to scCDC function from the scCDC package. It is a list with 3 elements: Detection, Quantification and Correction, which are lists of arguments to pass to the corresponding functions from the scCDC package: scCDC::ContaminationDetection, scCDC::ContaminationQuantification and scCDC::ContaminationCorrection.
keep_contam_assay: Whether to keep the Contaminated assay (the original counts before contamination correction) in the object. If FALSE (default), the assay is dropped right after the correction to save memory.
log: Logger

Value

A Seurat object with contaminant RNA corrected counts in the "RNA" assay, the original counts in the "Contaminated" assay (unless keep_contam_assay is FALSE), and the tool used in @misc$contamination$tool. For scCDC, the detected GCGs and contamination ratios are recorded in @misc$contamination as well.