empty_droplets_fn: Calculate empty droplet statistics for each cell.

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

Calculate empty droplet statistics for each cell.

Description

See DropletUtils::emptyDrops() for implementation details.

Usage

empty_droplets_fn(
  sce_raw,
  empty_droplets_lower,
  empty_droplets_enabled = TRUE,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

sce_raw	(input target) A SingleCellExperiment object.
empty_droplets_lower	An integer scalar: lower bound on the total UMI count at or below which all barcodes are assumed to correspond to empty droplets. Passed to DropletUtils::emptyDrops().
empty_droplets_enabled	A logical scalar: if TRUE, skip empty droplets calculation and return NULL.
BPPARAM	A BiocParallel::BiocParallelParam object.

Value

A DataFrame object (value returned from DropletUtils::emptyDrops()) if empty_droplets_enabled is TRUE, NULL otherwise. Output target: empty_droplets

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