Normalise Baits

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Description

Calculate normalisation factors s_j for each bait.

Usage

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normaliseBaits(cd, normNcol = "NNb", shrink = FALSE,
      plot = TRUE, outfile = NULL, debug = FALSE)

Arguments

cd

A chicagoData object.

normNcol

The name of the column in cd that contains normalised counts.

shrink

Deprecated.

plot

If TRUE, 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.

debug

Deprecated.

Details

A chicagoData object: intData(cd) gains a new column s_j, and normalised output NNb (unless the normNcol parameter is altered).

Value

An object of class chicagoData.

Warning

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

Author(s)

Mikhail Spivakov, Jonathan Cairns, Paula Freire Pritchett

Examples

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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 <- normaliseBaits(cdUnitTest)