estimateBrownianComponent {Chicago} | R Documentation |
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.)
estimateBrownianNoise(cd)
cd |
A |
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
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)