MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments

Description

The MSProcessedImagingExperiment class is a simple extension of MSImagingExperiment for sparse spectra. All methods for that class apply. In addition, each data element must be stored as a column-major sparse_mat.

Methods

All methods for MSImagingExperiment also work on MSProcessedImagingExperiment objects. Additional methods are documented below:

intensityData(object), intensityData(object) <- value:

Get or set the underlying (pre-binned) intensity values associated with the sparse mass spectra.

mzData(object), mzData(object) <- value:

Get or set the underlying (pre-binned) m/z values associated with the sparse mass spectra.

mz(object) <- value:

Setting the m/z values changes the m/z binning scheme for the entire dataset (without modifying the underlying data).

resolution(object) <- value:

Setting the m/z resolution changes the m/z binning scheme for the entire dataset (without modifying the underlying data).

tolerance(object), tolerance(object) <- value:

Get or set the binning tolerance for sparse spectra or peaks.

combiner(object), combiner(object) <- value:

Get or set the binning function for sparse spectra or peaks.

pull(x, ..., as.matrix=FALSE):

Pull all data elements of imageData into memory as sparse matrices.

Author(s)

Kylie A. Bemis

See Also

MSImagingExperiment, MSContinuousImagingExperiment