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Import scRNA-seq data.

Source: R/single_sample_input_qc.R
sce_raw_fn.Rd

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

    • "spaceranger": a raw feature-barcode matrix from 10x Genomics spaceranger

    • "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