ImagingExperiment-class: ImagingExperiment: Abstract class for imaging experiments

Description Slots Methods Author(s) See Also Examples

Description

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.

Slots

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.

Methods

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.

Author(s)

Kylie A. Bemis

See Also

SparseImagingExperiment, MSImagingExperiment

Examples

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

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

removeClass("MyImagingExperiment")

Cardinal documentation built on Nov. 8, 2020, 11:10 p.m.