normalize-methods {Cardinal} | R Documentation |
Apply normalization to a mass spectrometry imaging dataset.
## S4 method for signature 'MSImageSet' normalize(object, method = "tic", ..., pixel = pixels(object), plot = FALSE) ## TIC normalization normalize.tic(x, tic=length(x), ...)
object |
An object of class |
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. |
x |
The mass spectrum to be normalized. |
tic |
The value to which to normalize the total ion current. |
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.
An object of class MSImageSet
with the normalized spectra.
Kylie A. Bemis
data <- generateImage(as="MSImageSet") normalize(data, method="tic", plot=interactive())