peakPick-methods {Cardinal} | R Documentation

## Peak Pick an Imaging Dataset

### Description

Apply peak picking to a mass spectrometry imaging dataset.

### Usage

    ## S4 method for signature 'MSImageSet'
    peakPick(object, method = c("simple", "adaptive", "limpic"),
        ...,
        pixel = pixels(object),
        plot = FALSE)

    ## Local maxima and SNR with constant noise
    peakPick.simple(x, SNR=6, window=5, blocks=100, ...)

    ## Local maxima and SNR with adaptive noise
    peakPick.adaptive(x, SNR=6, window=5, blocks=100, spar=1, ...)

    ## LIMPIC peak detection
    peakPick.limpic(x, SNR=6, window=5, blocks=100, thresh=0.75, ...)

### Arguments

`object` | An object of class `MSImageSet`.
`method` | The peak picking method to use.
`pixel` | The pixels to peak pick. 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 peak picking method.
`x` | The mass spectrum to be peak picked.
`SNR` | The minimum signal-to-noise ratio to be considered a peak.
`window` | The window width for seeking local maxima.
`blocks` | The number of blocks in which to divide the mass spectrum in order to calculate the noise.
`spar` | Smoothing parameter for the spline smoothing applied to the spectrum in order to decide the cutoffs for throwing away false noise spikes that might occur inside peaks.
`thresh` | The thresholding quantile to use when comparing slopes in order to throw away peaks that are too flat.

### Details

Peak picking 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 `list` with two vectors of the same length as `x`:

- `peaks`: A `logical` vector indicating peaks.

- `noise`: A `numeric` vector with the estimated noise.

Internally, `pixelApply` is used to apply the peak picking. See its documentation page for more details on additional objects available to the environment installed to the peak picking function.

### Value

An object of class `MSImageSet` with the peak picking spectra.

### Author(s)

Kylie A. Bemis

### References

Mantini, D., Petrucci, F., Pieragostino, D., Del Boccio, P., Di Nicola, M., Di Ilio, C., et al. (2007). LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise. BMC Bioinformatics, 8(101), 101. doi:10.1186/1471-2105-8-101

### See Also

`MSImageSet`, `peakAlign`, `peakFilter`, `reduceDimension`, `pixelApply`

### Examples

    data <- generateImage(as="MSImageSet")
    peakPick(data, method="simple", plot=interactive())

[Package Cardinal version 1.12.1 Index]