estimateBrownianComponent: Estimate Brownian background component.
In Chicago: CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Description Usage Arguments Value Warning Author(s) See Also Examples

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.)

1	estimateBrownianNoise(cd)

`cd`	A `chicagoData` object.

An object of class chicagoData.

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

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

chicagoPipeline

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)