Function for discriminating "Cell" barcodes from "Dead" cells and "Debris" based on hard cut-offs for UMI transcript & gene content, and percent mitochondrial UMIs

This function designates high transcript/gene content & low percent mitochondrial content barcodes as "Cell", high percent mitochondrial content barcodes as "Dead", & low transcript/gene content barcodes as "Debris"

scprep_cell_filter(
  dataset = dataset,
  sample = sample,
  min_umi = 100,
  min_gene = 0,
  max_mito = 0.2
)

Arguments

dataset

ExpressionSet, Seurat, or SingleCellExperiment object with scRNA data

sample

Sample ID stored under "Sample" in metadata slot

min_umi

UMI transcript threshold

min_gene

Genes detected threshold

max_mito

Percent mitochondrial transcript threshold (0 = No mito transcripts allowed, 1 = No limit for mito transcripts)

Value

Sample-specific Cell, Dead, & Debris assignment

Examples

if (FALSE) {
# Assuming you have an ExpressionSet object called 'eset' and sample name
scprep_cell_filter(dataset=eset, sample="Sample1", min_umi=100, min_gene=0, max_mito=0.2)
}