Extract QC parameters from the SingleCellExperiment object — getSceParams • singleCellTK

Extract QC parameters from the SingleCellExperiment object

getSceParams(
  inSCE,
  skip = c("runScrublet", "runDecontX", "runBarcodeRanksMetaOutput", "genesets",
    "runSoupX"),
  ignore = c("algorithms", "estimates", "contamination", "z", "sample", "rank",
    "BPPARAM", "batch", "geneSetCollection", "barcodeArgs"),
  directory = "./",
  samplename = "",
  writeYAML = TRUE
)

Arguments

inSCE: A SingleCellExperiment object.
skip: Skip extracting the parameters of the provided QC functions.
ignore: Skip extracting the content within QC functions.
directory: The output directory of the SCTK_runQC.R pipeline.
samplename: The sample name of the SingleCellExperiment objects.
writeYAML: Whether output yaml file to store parameters. Default if TRUE. If FALSE, return character object.

Value

If writeYAML TRUE, a yaml object will be generated. If FALSE, character object.