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 1.15.0 Index]