ImagingExperiment-class {Cardinal} | R Documentation |
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.
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.
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
.
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("MyImageSet")