normalize-methods {Cardinal} | R Documentation |
Apply normalization to the feature vectors of an imaging dataset.
## S4 method for signature 'SparseImagingExperiment' normalize(object, method = c("tic", "rms", "reference"), ...) ## S4 method for signature 'MSImageSet' normalize(object, method = "tic", ..., pixel = pixels(object), plot = FALSE) ## Totial-ion-current normalization normalize.tic(x, tic=length(x), ...) ## Root-mean-square normalization normalize.rms(x, rms=1, ...) ## Reference normalization normalize.reference(x, feature, scale=1, ...)
object |
An imaging dataset. |
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 each pixel while it is being processed? |
... |
Additional arguments passed to the normalization method. |
x |
The signal to be normalized. |
tic |
The value to which to normalize the total ion current. |
rms |
The value to which to normalize the root-mean-square. |
feature |
The feature to use as a reference for normalization. |
scale |
The value to which to normalize the reference. |
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 the same class with the normalized spectra.
Kylie A. Bemis
MSImagingExperiment
,
MSImageSet
,
pixelApply
,
process
setCardinalBPPARAM(SerialParam()) set.seed(2) data <- simulateImage(preset=1, npeaks=10, dim=c(3,3)) data <- data[,pData(data)$circle] # queue normalization data <- normalize(data, method="tic") # apply normalization data_normalized <- process(data)