peakFilter-methods {Cardinal} | R Documentation

## Peak filter or mass filter an imaging dataset

### Description

Apply peak filtering or mass filtering to a mass spectrometry imaging dataset.

### Usage

    ## S4 method for signature 'MSImagingExperiment'
    mzFilter(object, ..., freq.min = 0, thresh.max = 0.01)

    ## S4 method for signature 'MSImagingExperiment'
    peakFilter(object, ..., freq.min = 0.01, thresh.max = 0)

    ## 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, ...)

### Arguments

`object` | An object of class `MSImageSet`.
`freq.min` | Minimum frequency; peaks that occur in the dataset in lesser proportion than this will be dropped.
`thresh.max` | Minimum threshold relative to maximum mean intensity; features with mean intensity lesser than this, as a proportion of the maximum intensity in the mean spectrum, 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.

### Details

When applied to a `MSImagingExperiment` object, `peakFilter` uses the `summarize()` to generate useful statistics about the detected peaks. These include the ‘min’, ‘max’, ‘mean’, ‘sum’, ‘sd’, and ‘var’ of the detected peaks. These can be used in logical expressions to filter the peaks.

Note that `mzFilter` is an alias for `peakFilter`, with different default parameters that are more appropriate for data that has not been peak picked and aligned.

When applied to a `MSImageSet` object, 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 the same class with the filtered peaks.

### Author(s)

Kylie A. Bemis

### See Also

`MSImagingExperiment`, `MSImageSet`, `peakPick`, `peakAlign`, `peakBin`, `reduceDimension`, `featureApply`, `process`

### Examples

    register(SerialParam())

    set.seed(2)
    data <- simulateImage(preset=1, npeaks=10, dim=c(3,3))
    data <- data[,pData(data)$circle]

    # queue peak picking, alignment, and filtering
    data <- peakPick(data, method="simple", SNR=6)
    data <- peakAlign(data, tolerance=200, units="ppm")
    data <- peakFilter(data, freq.min=0.2)

    # apply peak picking, alignment, and filtering
    data_peaks <- process(data, plot=interactive())

[Package Cardinal version 2.2.6 Index]