clean.counts: Filter counts matrix

In hms-dbmi/scde: Single Cell Differential Expression

Filter counts matrix

Description

Filter counts matrix based on gene and cell requirements

Usage

clean.counts(counts, min.lib.size = 1800, min.reads = 10,
  min.detected = 5)

Arguments

counts	read count matrix. The rows correspond to genes, columns correspond to individual cells
min.lib.size	Minimum number of genes detected in a cell. Cells with fewer genes will be removed (default: 1.8e3)
min.reads	Minimum number of reads per gene. Genes with fewer reads will be removed (default: 10)
min.detected	Minimum number of cells a gene must be seen in. Genes not seen in a sufficient number of cells will be removed (default: 5)

Value

a filtered read count matrix

Examples

data(pollen)
dim(pollen)
cd <- clean.counts(pollen)
dim(cd)

hms-dbmi/scde documentation built on April 19, 2023, 10:21 p.m.