qcInputProcess: Create SingleCellExperiment object from command line input...

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

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

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.