Chicago (version 1.0.3)

estimateTechnicalNoise: Estimate Technical Noise

Description

Calculates the expected technical noise based on trans read pairs.

Usage

estimateTechnicalNoise(cd, plot = TRUE, outfile = NULL)

Arguments

cd

A chicagoData object.

plot

Logical - if TRUE, then output a diagnostic plot.

outfile

NULL, or a character string. If NULL, the diagnostic plot is outputted to the current plotting device. If a character string, e.g. outfile="tech.pdf", then the plot will be outputted to that file.

Value

An object of class chicagoData, with additional columns "tlb", "tblb", "Tmean".

Warning

The object intData(cd) 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)

cdUnitTest <- estimateTechnicalNoise(cdUnitTest)