fitBackVar: Function for computing a background model of gene expression...

In RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Function for computing a background model of gene expression variability

Description

This funtion fits a second order polynomial to the variance-mean dependence across all genes in log space.

Usage

fitBackVar(x, mthr = -1)

Arguments

x	Matrix of transcript counts with genes as rows and cells as columns.
mthr	Real number. Threshold of log2 mean expression. Genes with mean expression < mthr are discarded prior to fitting the polynomial. Default is -1.

Value

List object of four components:

fit	model fit as returned by the lm function.
genes	genes with expression variance greater than the polynomial fit.
m	mean expression of all genes
v	expression variance of all genes

Examples

bg <- fitBackVar(intestinalDataSmall)

RaceID documentation built on April 4, 2025, 4:34 a.m.