Skip to contents

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

Source: R/single_sample_input_qc.R
get_gene_filter.Rd

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.