MSImagingExperiment-class {Cardinal}R Documentation

MSImagingExperiment: Mass spectrometry imaging experiments

Description

The MSImagingExperiment class is designed for mass spectrometry imaging experimental data and metadata. It is designed to contain full MSI experiments, including multiple runs and replicates, potentially across multiple files. Both 2D and 3D imaging experiments are supported, as well as any type of experimental metadata such as diagnosis, subject, time point, etc.

Usage

## Instance creation
MSImagingExperiment(
    imageData = matrix(nrow=0, ncol=0),
    featureData = MassDataFrame(),
    pixelData = PositionDataFrame(),
    metadata = list(),
    processing = SimpleList(),
    centroided = FALSE)

## Additional methods documented below

Arguments

imageData

Either a matrix-like object with number of rows equal to the number of features and number of columns equal to the number of pixels, or an ImageArrayList.

featureData

A MassDataFrame with feature metadata, with a row for each m/z value.

pixelData

A PositionDataFrame with pixel metadata, with a row for each pixel.

metadata

A list with experimental-level metadata.

processing

A SimpleList with processing steps. This should typically be empty for new objects.

centroided

FALSE if the object contains profile spectra and TRUE if the spectra have been peak-picked and centroided.

Details

The MSImagingExperiment class is designed as a replacement for the MSImageSet class, using a simplified, robust implementation that should be more future-proof and enable better support for large, high-resolution experiments, multimodal experiments, and experiments with specialized needs such as non-gridded pixel coordinates.

Subclasses MSContinuousImagingExperiment and MSProcessedImagingExperiment exist to allow downstream methods to make assumptions about the underlying data storage (dense matrices for 'continous' format and sparse matrices for 'processed' format), which can sometimes allow more efficient computations.

Slots

imageData:

An object inheriting from ImageArrayList, storing one or more array-like data elements with conformable dimensions.

featureData:

Contains feature information in a MassDataFrame. Each row includes the metadata associated with an m/z value.

elementMetadata:

Contains pixel information in a PositionDataFrame. Each row includes the metadata for a single observation (e.g., a pixel), including specialized slot-columns for tracking pixel coordinates and experimental runs.

metadata:

A list containing experiment-level metadata.

processing:

A SimpleList containing processing steps (including both queued and previously executed processing steps).

centroided:

FALSE if the object contains profile spectra and TRUE if the spectra have been peak-picked and centroided.

Methods

All methods for ImagingExperiment and SparseImagingExperiment also work on MSImagingExperiment objects. Additional methods are documented below:

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

Get or set the m/z values from pixelData.

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

Get or set the m/z resolution of the dataset. Typically, this should not be set manually.

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

Get or set the spectra (alias for iData(object)).

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

Get or set the peaks of a centroided experiment (alias for iData(object) for centroided datasets only).

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

Get or set the spatial position slot-columns from pixelData.

pixels(object, ..., coord, run):

Returns the row indices of pixelData corresponding to conditions passed via ....

features(object, ..., mz):

Returns the row indices of featureData corresponding to conditions passed via ....

collect(x, ...):

Pull all data elements of imageData into memory as matrices.

msiInfo(object, ...):

Returns metadata for writing the object to imzML.

rbind(...), cbind(...):

Combine MSImagingExperiment objects by row or column.

Author(s)

Kylie A. Bemis

See Also

ImagingExperiment, SparseImagingExperiment, MSContinuousImagingExperiment, MSProcessedImagingExperiment

Examples

mz <- mz(from=200, to=220, by=400)
coord <- expand.grid(x=1:3, y=1:3)
data <- matrix(runif(length(mz) * nrow(coord)),
    nrow=length(mz), ncol=nrow(coord))

idata <- ImageArrayList(data)
fdata <- MassDataFrame(mz=mz)
pdata <- PositionDataFrame(coord=coord)

x <- MSImagingExperiment(
    imageData=idata,
    featureData=fdata,
    pixelData=pdata)

print(x)

[Package Cardinal version 2.2.2 Index]