getSceParams: Extract QC parameters from the SingleCellExperiment object

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Extract QC parameters from the SingleCellExperiment object

Description

Extract QC parameters from the SingleCellExperiment object

Usage

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.

compbiomed/singleCellTK documentation built on May 8, 2024, 6:58 p.m.