sce_rm_doublets_fn: Remove cell doublets from a 'SingleCellExperiment' object.

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

Remove cell doublets from a SingleCellExperiment object.

Description

Remove cell doublets from a SingleCellExperiment object.

Usage

sce_rm_doublets_fn(sce_norm_hvg, doublet_density, max_doublet_score)

Arguments

sce_norm_hvg	(input target) A SingleCellExperiment object.
doublet_density	(input target) A numeric vector.
max_doublet_score	A numeric scalar: cells with doublet score (log10(doublet_density + 1)) exceeding this value will be marked as doublets and removed from sce_norm_hvg. If NULL, cells won't be filtered out.

Value

A modified sce_norm_hvg object with removed cell doublets.

The following items of metadata(sce_norm_hvg) are added or modified:

• has_filtered_doublets: TRUE if max_doublet_score is not NULL.

• max_doublet_score: the value of max_doublet_score function argument.

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