sce_valid_cells_fn: Subset cells in a 'SingleCellExperiment' object to non-empty...

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

Subset cells in a SingleCellExperiment object to non-empty ones and add corresponding statistics.

Description

Subset cells in a SingleCellExperiment object to non-empty ones and add corresponding statistics.

Usage

sce_valid_cells_fn(sce_raw, empty_droplets, empty_droplets_fdr_threshold)

Arguments

sce_raw	(input target) A SingleCellExperiment object.
empty_droplets	(input target) A DataFrame object returned from DropletUtils::emptyDrops().
empty_droplets_fdr_threshold	A numeric scalar: threshold value for FDR of a cell being empty.

Value

A subsetted sce_raw object. Output target: sce_valid_cells

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.