sce_raw_fn: Import scRNA-seq data.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Import scRNA-seq data.

Description

For more details see the INPUT_DATA parameter in vignette("stage_input_qc").

Usage

sce_raw_fn(input_data, input_data_subset = NULL)

Arguments

input_data

A named list of named lists containing character scalars: type: "cellranger": a raw feature-barcode matrix from 10x Genomics cellranger "table": a delimited text file (table) "sce": a SingleCellExperiment object (Rds file) "sce_drake_cache": a SingleCellExperiment object loaded from a drake cache path: a path to input file (or directory in case of type = "cellranger") delimiter: a field delimiter when type = "table" target_name: a name of SingleCellExperiment target when type = "sce_drake_cache"

input_data_subset

NULL or a named list by which subsetting of the imported data will be performed. The list must contain the following items: subset_by (character scalar): name of column in colData() to use for subsetting values (vector): values to subset to negate (logical scalar): if TRUE, negate the selection

Value

A SingleCellExperiment object. Output target: sce_raw

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.