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 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

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

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

    removeClass("MyImagingExperiment")

[Package Cardinal version 2.12.0 Index]