% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sctkQCUtils.R
 \name{qcInputProcess}
 \alias{qcInputProcess}
 \title{Create SingleCellExperiment object from command line input arguments}
 \usage{
 qcInputProcess(
   preproc,
   samplename,
   path,
   raw,
   fil,
   ref,
   rawFile,
   filFile,

   flatFiles,

   dataType
 )
 }
 \arguments{

 \item{preproc}{Method used to preprocess the data. It's one of the path provided in --preproc argument.}
 

 \item{samplename}{The sample name of the data. It's one of the path provided in --sample argument.}
 
 \item{path}{Base path of the dataset. It's one of the path provided in --bash_path argument.}
 
 \item{raw}{The directory contains droplet matrix, gene and cell barcodes information. It's one of the path provided in --raw_data_path argument.}
 
 \item{fil}{The directory contains cell matrix, gene and cell barcodes information. It's one of the path provided in --cell_data_path argument.}
 
 \item{ref}{The name of reference used by cellranger. Only need for CellrangerV2 data.}
 
 \item{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.}
 
 \item{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.}
 

 \item{flatFiles}{The full paths of the matrix, barcode, and features (in that order) files used to construct an SCE object.}
 

 \item{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 \link[SingleCellExperiment]{SingleCellExperiment} object containing
 the droplet or cell data or both,depending on the dataType that users provided.
 }
 \description{
 Create SingleCellExperiment object from command line input arguments
 }