peakFilter-methods {Cardinal} | R Documentation |
Apply peak filtering to a mass spectrometry imaging dataset.
## S4 method for signature 'MSImagingExperiment' peakFilter(object, freq.min = 0.01, ...) ## S4 method for signature 'MSImageSet' peakFilter(object, method = "freq", ..., pixel, plot) ## Filter based on the frequency of a peak peakFilter.freq(x, freq.min=0.01, ...)
object |
An object of class |
freq.min |
Peaks that occur in the dataset in lesser proportion than this will be dropped. |
... |
Additional arguments passed to the peak filtering method, or conditions evaluating to logical vectors where only those conditions that are TRUE are retained. |
method |
The peak filtering method to use. |
pixel |
Deprecated. |
plot |
Deprecated. (Never did anything anyway.) |
x |
The vector of ion image intensities to filter. |
Unlike most other processing methods, peakFilter
operates on the feature space (ion images) of the dataset.
Peak filtering 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
: The vector of ion image intensities to filter.
...
: Additional arguments.
A user-created function should return a logical: TRUE
means keep the peak, and FALSE
means remove the peak.
Internally, featureApply
is used to apply the filtering. See its documentation page for more details on additional objects available to the environment installed to the peak filtering function.
An object of the same class with the filtered peaks.
Kylie A. Bemis
MSImageSet
,
MSImagingExperiment
,
peakPick
,
peakAlign
,
peakBin
,
reduceDimension
,
featureApply
,
process
data <- generateImage(diag(2), as="MSImageSet") peaks <- peakPick(data, method="simple", plot=interactive()) peaks <- peakAlign(peaks, method="diff", plot=interactive()) peaks <- peakFilter(peaks, method="freq")