normalize-methods: Normalize an Imaging Dataset

Description

Apply normalization to a mass spectrometry imaging dataset.

Usage

"normalize"(object, method = "tic",
	...,
	pixel = pixels(object),
	plot = FALSE)
## TIC normalization
normalize.tic(x, tic=length(x), ...)

Arguments

object

An object of class MSImageSet.

method

The normalization method to use.

pixel

The pixels to normalize. If less than the extent of the dataset, this will result in a subset of the data being processed.

plot

Plot the mass spectrum for each pixel while it is being processed?

...

Additional arguments passed to the normalization method.

The mass spectrum to be normalized.

tic

The value to which to normalize the total ion current.

Value

An object of class MSImageSet with the normalized spectra.

Details

Normalization is usually performed using the provided functions, but a user-created function can also be passed to method. In this case it should take the following arguments:

x: A numeric vector of intensities.
...: Additional arguments.

A user-created function should return a numeric vector of the same length.

Internally, pixelApply is used to apply the normalization. See its documentation page for more details on additional objects available to the environment installed to the normalization function.

Examples

Run this code

data <- generateImage(as="MSImageSet")
normalize(data, method="tic", plot=interactive())