msiSlices {MALDIquant}

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

Description

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).

Usage

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

Value

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 [e-mail]

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