R: Normalise Baits

normaliseBaits {Chicago}

R Documentation

Normalise Baits

Description

Calculate normalisation factors s_j for each bait.

Usage

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

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)

[Package Chicago version 1.8.0 Index]