reduceNoise: Reduce noise in single-cell data

In cellGeometry: Geometric Single Cell Deconvolution

Reduce noise in single-cell data

Description

Simple filter for removing noise in single-cell data.

Usage

reduceNoise(cellmat, noisefilter = 2, noisefraction = 0.25)

Arguments

cellmat	Matrix of log2 mean gene expression in rows with cell types in columns.
noisefilter	Sets an upper bound for noisefraction cut-off below which gene expression is set to 0. Essentially gene expression above this level must be retained in the signature. Setting this higher can allow more suppression via noisefraction and can favour more highly expressed genes.
noisefraction	Numeric value. Maximum mean log2 gene expression across cell types is calculated and values in celltypes below this fraction are set to 0. Set in conjunction with noisefilter. Note: if this is set too high (too close to 1), it can have a deleterious effect on deconvolution.

Value

Filtered mean gene expression matrix with genes in rows and cell types in columns.

cellGeometry documentation built on April 20, 2026, 1:06 a.m.