mzAlign-methods: Mass align an imaging dataset

In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Description

Apply spectral alignment to a mass spectrometry imaging dataset.

Usage

## S4 method for signature 'MSImagingExperiment,numeric'
mzAlign(object, ref, tolerance = NA, units = c("ppm", "mz"),
        span = 0.75, control = loess.control(), ...)

## S4 method for signature 'MSImagingExperiment,missing'
mzAlign(object, tolerance = NA, units = c("ppm", "mz"),
        span = 0.75, control = loess.control(), quantile = 0.2, ...)

Arguments

object	An imaging dataset.
ref	A reference to which to align the spectra.
tolerance	The tolerance to be used when matching the peaks in the unaligned spectra to the reference spectrum. If this is NA, then automatically guess a tolerance from the data.
units	The units to use for the tolerance.
span	The smoothing parameter for the local polynomial regression used to determine the warping function.
control	Additional control parameters for the local polynomial regression used to determine the warping function. See loess.control.
quantile	The top quantile of reference points (peaks detected via local maxima) to use from the reference spectrum.
...	Ignored.

Details

Mass alignment is performed against a vector of reference m/z values of expected peaks. The nearest local maxima to the reference peaks are detected in each unaligned spectrum (within tolerance), and then the unaligned spectra are warped to maximize correlation with the reference spectrum.

If no reference peaks are provided, then the mean spectrum is calculated instead, and reference peaks are selected by detecting local maxima. Some number of these reference points with the highest intensities (determined by quantile) are then used as the reference for alignment.

Internally, pixelApply is used to perform the alignment. See its documentation page for more details.

Value

An object of the same class with the aligned spectra.

Author(s)

Kylie A. Bemis

See Also

MSImagingExperiment, mzBin, peakAlign, pixelApply, process

Examples

setCardinalBPPARAM(SerialParam())

set.seed(2)
data <- simulateImage(preset=1, npeaks=10, dim=c(3,3), sdmz=500)
data <- data[,pData(data)$circle]

# queue spectral alignment
data <- mzAlign(data, tolerance=1, units="mz")

# apply spectral alignment
data_aligned <- process(data, plot=interactive())

Cardinal documentation built on Nov. 8, 2020, 11:10 p.m.