Create SingleCellExperiment object from command line input arguments

qcInputProcess(
  preproc,
  samplename,
  path,
  raw,
  fil,
  ref,
  rawFile,
  filFile,
  dataType
)

Arguments

preproc: Method used to preprocess the data. It's one of the path provided in --preproc argument.
samplename: The sample name of the data. It's one of the path provided in --sample argument.
path: Base path of the dataset. It's one of the path provided in --bash_path argument.
raw: The directory contains droplet matrix, gene and cell barcodes information. It's one of the path provided in --raw_data_path argument.
fil: The directory contains cell matrix, gene and cell barcodes information. It's one of the path provided in --cell_data_path argument.
ref: The name of reference used by cellranger. Only need for CellrangerV2 data.
rawFile: The full path of the RDS file or Matrix file of the raw gene count matrix. It's one of the path provided in --raw_data argument.
filFile: The full path of the RDS file or Matrix file of the cell count matrix. It's one of the path provided in --cell_data argument.
dataType: Type of the input. It can be "Both", "Droplet" or "Cell". It's one of the path provided in --genome argument.

A list of SingleCellExperiment object containing the droplet or cell data or both,depending on the dataType that users provided.