fitBackVar {RaceID}

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)