qcInputProcess {singleCellTK} | R Documentation

## Create SingleCellExperiment object from command line input arguments

### Description

Create SingleCellExperiment object from command line input arguments

### Usage

    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.

### Value

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

[Package singleCellTK version 2.2.0 Index]