AnnotatedImagingExperiment-class: AnnotatedImagingExperiment: Mass spectrometry imaging...

In Cardinal: A mass spectrometry imaging toolbox for statistical analysis

Description

The AnnotatedImagingExperiment class is designed for mass spectrometry imaging experimental data and metadata. It is designed to contain full MSI experiments, including multiple runs and replicates, potentially across multiple files. Both 2D and 3D imaging experiments are supported, as well as any type of experimental metadata such as diagnosis, subject, time point, etc.

Usage

## AnnotatedImage list
AnnotatedImageList(...)

## Instance creation
AnnotatedImagingExperiment(
    imageData = AnnotatedImageList(),
    featureData = DataFrame(),
    phenoData = DataFrame(),
    metadata = list())

## Additional methods documented below

Arguments

...	Either Image or AnnotatedImage objects used to create the AnnotatedImageList.
imageData	An Image, an AnnotatedImage, or an AnnotatedImageList.
featureData	A DataFrame with feature metadata, with a row for each channel/frame.
phenoData	A DataFrame with phenotype metadata, with a row for each sample.
metadata	A list with experimental-level metadata.

Details

The AnnotatedImagingExperiment class is designed as a replacement for the MSImageSet class, using a simplified, robust implementation that should be more future-proof and enable better support for large, high-resolution experiments, multimodal experiments, and experiments with specialized needs such as non-gridded pixel coordinates.

Subclasses MSContinuousImagingExperiment and MSProcessedImagingExperiment exist to allow downstream methods to make assumptions about the underlying data storage (dense matrices for 'continous' format and sparse matrices for 'processed' format), which can sometimes allow more efficient computations.

Slots

imageData:

An object inheriting from AnnotatedImageList, storing one or more AnnotatedImage elements.

featureData:

Contains feature information in a DataFrame. Each row includes the metadata associated with frame/channel of the images.

elementMetadata:

Contains phenotype information in a DataFrame. Each row includes the metadata for a single observation (e.g., a sample).

metadata:

A list containing experiment-level metadata.

Methods

All methods for ImagingExperiment also work on AnnotatedImagingExperiment objects. Additional methods are documented below:

coord(object):

Get the absolute offsets of the top-left corner of the images.

resolution(object):

Get the pixel resolutions of the images. This corresponds to the number of pixels per unit step on the x/y axes when plotted.

height(x):

Get the heights of the images (as plotted).

width(x):

Get the widths of the images (as plotted).

Author(s)

Kylie A. Bemis

See Also

ImagingExperiment, AnnotatedImage

Examples

## Not run: 
x <- readImage(system.file('images', 'nuclei.tif', package='EBImage'))

y <- AnnotatedImagingExperiment(x)

print(y)

## End(Not run)

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