getSceParams {singleCellTK}

R Documentation

Extract QC parameters from the SingleCellExperiment object

Description

Extract QC parameters from the SingleCellExperiment object

Usage

getSceParams(
  inSCE,
  skip = c("scrublet", "runDecontX", "runBarcodeRanksMetaOutput"),
  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.

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