estimateBrownianComponent {Chicago} | R Documentation

## 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.

### Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

### 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)

[Package Chicago version 1.20.0 Index]