Cardinal (version 1.4.0)

peakPick-methods: Peak Pick an Imaging Dataset

Description

Apply peak picking to a mass spectrometry imaging dataset.

Usage

"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.

Value

An object of class MSImageSet with the peak picking spectra.

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.

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())