ImagingExperiment-class: ImagingExperiment: Abstract class for imaging experiments
In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Description Slots Methods Author(s) See Also Examples

The ImagingExperiment class is a virtual class for biological imaging experiments. It includes slots for sample/pixel metadata and for feature metadata. The class makes very few assumptions about the structure of the underlying imaging data, including the dimensions.

For a concrete subclass, see the SparseImagingExperiment class, which assumes that the image data can be represented as a matrix where columns represent pixels and rows represent features. The MSImagingExperiment subclass is further specialized for analysis of mass spectrometry imaging experiments.

imageData:: An object inheriting from ImageList, storing one or more array-like data elements. No assumption is made about the shape of the arrays.
featureData:: Contains feature information in a DataFrame. Each row includes the metadata for a single feature (e.g., a color channel, a molecular analyte, or a mass-to-charge ratio).
elementMetadata:: Contains sample or pixel information in a DataFrame. Each row includes the metadata for a single observation (e.g., a sample or a pixel).
metadata:: A list containing experiment-level metadata.

imageData(object), imageData(object) <- value:: Get and set the imageData slot.
iData(object, i), iData(object, i, ...) <- value:: Get or set the element i from the imageData. If i is missing, the first data element is returned.
phenoData(object), phenoData(object) <- value:: Get and set the elementMetadata slot.
sampleNames(object), sampleNames(object) <- value:: Get and set the row names of the elementMetadata slot.
pData(object), pData(object) <- value:: A shortcut for phenoData(object) and phenoData(object)<-.
pixelData(object), pixelData(object) <- value:: In subclasses where columns represent pixels, get and set the elementMetadata slot.
pixelNames(object), pixelNames(object) <- value:: In subclasses where columns represent pixels, get and set the row names of the elementMetadata slot.
featureData(object), featureData(object) <- value:: Get and set the featureData slot.
featureNames(object), featureNames(object) <- value:: Get and set the row names of the featureData slot.
fData(object), fData(object) <- value:: A shortcut for featureData(object) and featureData(object)<-.
dim:: The dimensions of the object, as determined by the number of features (rows in featureData) and the number of samples/pixels (rows in elementMetadata).
object$name, object$name <- value:: Get and set the name column in pixelData.
object[[i]], object[[i]] <- value:: Get and set the column i (a string or integer) in pixelData.
object[i, j, ..., drop]:: Subset based on the rows (fData) and the columns (pData). The result is the same class as the original object.
rbind(...), cbind(...):: Combine ImagingExperiment objects by row or column.

Kylie A. Bemis

SparseImagingExperiment, MSImagingExperiment

## cannot create an ImagingExperiment object
try(new("ImagingExperiment"))

## create an ImagingExperiment derived class
MyImagingExperiment <- setClass("MyImagingExperiment", contains="ImagingExperiment")
MyImagingExperiment()

removeClass("MyImagingExperiment")