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.

[Package singleCellTK version 2.0.0 Index]