ImagingExperiment-class {Cardinal}R Documentation

ImagingExperiment: Abstract class for imaging experiments

Description

The ImagingExperiment class is a virtual class for biological imaging experiments. It includes slots for 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 pixel information in a DataFrame. Each row includes the metadata for a single observation (e.g., 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.

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

Get and set the elementMetadata slot.

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

Get and set the row names of the elementMetadata slot.

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

A shortcut for pixelData(object) and pixelData(object)<-.

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)<-.

pixels(object, ...):

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

features(object, ...):

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

dim:

The dimensions of the object, as determined by the number of features (rows in featureData) and the number of pixels (rows in pixelData).

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.

Author(s)

Kylie A. Bemis

See Also

SparseImagingExperiment, MSImagingExperiment

Examples

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

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

removeClass("MyImageSet")

[Package Cardinal version 2.2.2 Index]