importImzMl {MALDIquantForeign}

Import imzML files

Description

This function imports files in imzML file format into MassSpectrum-class or MassPeaks-class objects.

Usage

importImzMl(path, coordinates = NULL, ...)

Arguments

path

character, path to directory or file which should be read in.

coordinates

matrix, 2 column matrix that contains the x- and y-coordinates for spectra that should be imported. Other spectra would be ignored.

...

arguments to be passed to import.

Value

a list of MassSpectrum-class or MassPeaks-class objects (depending on the centroided argument).

Author(s)

Sebastian Gibb

References

https://strimmerlab.github.io/software/maldiquant/,
Definition of imzML format: https://ms-imaging.org/imzml/

See Also

MassSpectrum-class, MassPeaks-class

Examples

library("MALDIquant")
library("MALDIquantForeign")

## get example directory
exampleDirectory <- system.file("exampledata", package="MALDIquantForeign")

## import
s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML"))

## import only spectra for pixel 1,1 and 2,1
s <- importImzMl(file.path(exampleDirectory, "tiny_continuous.imzML"),
                 coordinates = cbind(1:2, c(1, 1)))