peakFilter-methods {Cardinal} | R Documentation

## Peak Filter an Imaging Dataset

### Description

Apply peak filtering to a mass spectrometry imaging dataset.

### Usage

    ## S4 method for signature 'MSImageSet'
    peakFilter(object, method = "freq", ..., pixel, plot)

    ## Filter based on the frequency of a peak
    peakFilter.freq(x, freq.min=length(x) / 100, ...)

### Arguments

`object` | An object of class `MSImageSet`.
`method` | The peak filtering method to use.
`...` | Additional arguments passed to the peak filtering method.
`pixel` | Deprecated.
`plot` | Deprecated. (Never did anything anyway.)
`x` | The vector of ion image intensities to filter.
`freq.min` | Peaks that occur in the dataset fewer times than this will be removed.

### Details

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.

### Value

An object of class `MSImageSet` with the filtered peaks.

### Author(s)

Kylie A. Bemis

### See Also

`MSImageSet`, `peakPick`, `peakAlign`, `reduceDimension`, `featureApply`

### Examples

    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")

[Package Cardinal version 1.12.1 Index]