qcInputProcess {singleCellTK} | R Documentation |
Create SingleCellExperiment object from command line input arguments
qcInputProcess( preproc, samplename, path, raw, fil, ref, rawFile, filFile, dataType )
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.