Chicago (version 1.0.3)

estimateBrownianComponent: Estimate Brownian background component.

Description

Estimates the dispersion, and adds a a Bmean column giving the expected number of Brownian reads.

Usually, the dispersion is not calculated on the full dataset - rather, a subsample of baits is taken, and the dispersion is calculated on that. The number of baits used is taken from brownianNoise.subset (with an NA value meaning that the entire dataset is used, and no subsampling is performed).

(Note that the alias estimateBrownianNoise() is provided for back-compatibility.)

Usage

estimateBrownianNoise(cd)

Arguments

cd

A chicagoData object.

Value

An object of class chicagoData.

Warning

The object intData(x) is updated by reference. Thus, intData(cd) will be altered. See vignette for further information.

See Also

chicagoPipeline

Examples

data(cdUnitTest)

##modifications to cdUnitTest, ensuring it uses correct design directory
designDir <- file.path(system.file("extdata", package="Chicago"), "unitTestDesign")
cdUnitTest <- modifySettings(cd=cdUnitTest, designDir=designDir)

##make cdUnitTest use the full subset of baits
cdUnitTest <- modifySettings(cd=cdUnitTest, settings=list(brownianNoise.subset=NA))

cdUnitTest <- estimateBrownianComponent(cdUnitTest)