exportImzMl,MassSpectrum-method: Export to imzML files

Description

This function exports MassSpectrum-class objects into imzML files.

Usage

# S4 method for MassSpectrum
exportImzMl(x, file, force=FALSE, processed=TRUE,
coordinates=NULL, pixelSize=c(100, 100), ...)
# S4 method for list
exportImzMl(x, path, force=FALSE, processed=TRUE,
coordinates=NULL, pixelSize=c(100, 100), ...)

Arguments

x: a AbstractMassObject-class object or a list of AbstractMassObject-class objects.
file: character, file name.
force: logical, If TRUE the file would be overwritten or path would be created.
processed: logical, If TRUE (default) the spectra will be saved in processed mode (means mass and intensity is stored for each spectra separately in contrast to continuous mode where the mass is stored only for one spectrum).
coordinates: matrix, 2 column matrix that contains the x- and y-coordinates for the spectra.
pixelSize: numeric, a vector of length 2 that contains the x and y pixel size in micrometers (default: c(100, 100)).
path: character, path to directory in which the list of MassSpectrum-class would be exported. If path is a single filename all spectra will be exported to a single imzML file.
...: arguments to be passed to internal functions.

Author

Sebastian Gibb

References

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

Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, Laprevote O, Desbenoit N, Robbe M-F, Stoeckli M, Spengler B, Roempp A (2012)
imzML - A common data format for the flexible exchange and processing of mass spectrometry imaging data.
Journal of Proteomics 75 (16):5106-5110.
tools:::Rd_expr_doi("10.1016/j.jprot.2012.07.026")

Examples

Run this code


if (FALSE) {
library("MALDIquant")
library("MALDIquantForeign")

s <- list(createMassSpectrum(mass=1:5, intensity=1:5),
          createMassSpectrum(mass=1:5, intensity=1:5))

## export a list of spectra
exportImzMl(s, path="processed.imzML", coordinates=cbind(x=1:2, y=c(1, 1)))
}