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

Description Usage Arguments Value

View source: R/sctkQCUtils.R

Description

Create SingleCellExperiment object from command line input arguments

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
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.


singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.