msiSlices-functions function

Turn a list of AbstractMassObjects into a mass spectrometry imaging slice.

This function turns a mass spectrometry imaging dataset represented by a list of AbstractMassObject objects into an intensityMatrix for each slice (stored in an array).

msiSlices(x, center, tolerance, method=c("sum", "mean", "median"), adjust=TRUE)

Arguments

• x: a list of MassSpectrum/ MassPeaks objects.
• center: double, the center mass value of each slice.
• tolerance: double, specifies the thickness of the slices (center + c(-tolerance, tolerance)).
• method: used aggregation function.
• adjust: logical, if TRUE the lowest coordinates of the mass spectrometry imaging dataset are set to c(x=1, y=1) to avoid NA values at the borders.

Details

Each MassSpectrum/MassPeaks object in x must contain a list named imaging with an element pos that stores the x and y value of the spectrum, e.g.:

> metaData(spectra[[1]])$imaging$pos
x y
1 5

Returns

Returns an array of three dimensions. The first and second dimensions contains the x and y coordinates of the image. The third dimension represents the index of the center of each slice. There are two additional attributes, namely "center" and "tolerance" which store the original center and tolerance information.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

AbstractMassObject, MassSpectrum, MassPeaks, coordinates,AbstractMassObject-method, plotMsiSlice,list-method

Please find real examples on:

Website: https://strimmerlab.github.io/software/maldiquant/

Vignette: https://github.com/sgibb/MALDIquantExamples/raw/master/inst/doc/nyakas2013.pdf

Shiny: https://github.com/sgibb/ims-shiny/

Examples

## load package
library("MALDIquant")

## load example data
data("fiedler2009subset", package="MALDIquant")

## please note: this is NOT a MSI data set
## we just add some coordinates for demonstration
coordinates(fiedler2009subset) <- cbind(x=rep(1:4, 2), y=rep(1:2, each=4))

slices <- msiSlices(fiedler2009subset, center=c(5864.49, 8936.97),
                    tolerance=0.25)

slices