get_gene_filter: Get a logical filter for genes not passing a ratio of cells...

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

Get a logical filter for genes not passing a ratio of cells expressing a gene and a minimum number of UMI per gene.

Description

A gene is considered expressed when number of its UMIs across all cells is greater than min_umi and at the same time it is expressed in at least min_ratio_cells ratio of cells.

Usage

get_gene_filter(sce, min_ratio_cells, min_umi)

Arguments

sce	A SingleCellExperiment object.
min_ratio_cells	A numeric scalar: minimum ratio of cells expressing a gene.
min_umi	A numeric scalar: minimum number of UMI per gene across all cells.

Value

A logical vector of length nrow(sce): TRUE for genes not passing the filter, FALSE otherwise. This is for consistency with cell filters, e.g. the qc_filter target, where TRUE means the same as here, i.e. a cell is not passing the filter.

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