MSImageSet-class {Cardinal} | R Documentation |
Container for mass spectrometry imaging experimental data and metadata. MSImageSet
is derived from iSet
through SImageSet
. It extends these classes with information about the processing and analysis, requiring MIAPE-Imaging in its experimentData slot.
## Instance creation MSImageSet( spectra = Hashmat(nrow=0, ncol=0), mz = seq_len(dim(spectra)[1]), coord = expand.grid( x = seq_len(prod(dim(spectra)[-1])), y = seq_len(ifelse(prod(dim(spectra)[-1]) > 0, 1, 0))), imageData = MSImageData(data=spectra, coord=coord), pixelData = IAnnotatedDataFrame( data=coord, varMetadata=data.frame(labelType=rep("dim", ncol(coord)))), featureData = AnnotatedDataFrame( data=data.frame(mz=mz)), processingData = new("MSImageProcess"), protocolData = AnnotatedDataFrame( data=data.frame(row.names=sampleNames(pixelData))), experimentData = new("MIAPE-Imaging"), ...) ## Additional methods documented below
spectra |
A matrix-like object with number of rows equal to the number of features and number of columns equal to the number of non-missing pixels. Each column should be a mass spectrum. Alternatively, a multidimensional array that represents the datacube with the first dimension as the features (m/z values) can also be supplied. Additional dimensions could be the spatial dimensions of the image, for example. |
mz |
A numeric vector representing the mass-to-charge ratio features (m/z values) corresponding to the rows in the |
coord |
A |
imageData |
An object of class |
pixelData |
An object of class |
featureData |
An object of class |
processingData |
An object of class |
protocolData |
An object of class |
experimentData |
An object derived from class |
... |
Additional arguments passed to the initializer. |
imageData
:An instance of SImageData
, which stores one or more matrices of equal number of dimensions as elements in an 'immutableEnvironment'. This slot preserves copy-on-write behavior when it is modified specifically, but is pass-by-reference otherwise, for memory efficiency.
pixelData
:Contains pixel information in an IAnnotatedDataFrame
. This includes both pixel coordinates and phenotypic and sample data. Its rows correspond to the columns in imageData
.
featureData
:Contains variables describing features. Its rows correspond to the rows in imageData
in an IAnnotatedDataFrame
.
processingData
:Contains details about the pre-processing steps that have been applied to the spectra. An object of class MSImageProcess
.
experimentData
:Contains details of experimental methods. Must be MIAPE-Imaging
.
protocolData
:Contains variables describing the generation of the samples in pixelData
in an IAnnotatedDataFrame
.
.__classVersion__
:A Versions
object describing the version of the class used to created the instance. Intended for developer use.
SImageSet
, directly.
iSet
, by class "SImageSet", distance 1.
VersionedBiobase
, by class "iSet", distance 2.
Versioned
, by class "VersionedBiobase", distance 3.
MSImageSet
instances can be created through MSImageSet()
, but are more commonly created through reading of external data files.
Class-specific methods:
spectra(object), spectra(object) <- value
:Access and set the mass spectra in imageData
. This is a matrix-like object with rows corresponding to features and columns corresponding to pixels, so that each column of the returned object is a mass spectrum.
peaks(object), peaks(object) <- value
:Access and set the peaks in imageData
if peak picking have been performed. This is a shortcut for peakData(imageData(object))
. These are the unaligned peaks. Aligned peaks (if they exist) are accesed by spectra(object).
mz(object), mz(object) <- value
:Returns and sets the common m/z values of the mass spectra in the dataset. This is a required column of featureData
.
features(object, ..., mz)
:Access the feature indices (rows in featureData
) corresponding to variables in featureData
. Bisection search is used for fuzzy matching of m/z values.
pixels(object, ..., coord)
:Access the pixel indices (rows in pixelData
) corresponding to variables in pixelData
. If specified, coord
should be a data.frame
where each row corresponds to the coordinates of a desired pixel.
centroided(object), centroided(object) <- value
:Access whether the dataset consists of profile or centroided mass spectra. This is a shortcut for centroided(processingData(object))
. A setter is also provided, and is sometimes necessary for forcing some analysis methods to accept unprocessed spectra. (This is usually a bad idea.)
processingData(object), processingData(object) <- value
:Access and set the processingData
slot.
Standard generic methods:
combine(x, y, ...)
:Combine two or more MSImageSet
objects. Unique 'sample's in pixelData
are treated as a dimension.
MSImageSet[i, j, ..., drop]
:Subset an SImageSet
based on the rows (featureData components) and the columns (pixelData components). The result is a new MSImageSet
.
See iSet
and SImageSet
for additional methods.
Kylie A. Bemis
## Create an MSImageSet object spectra <- matrix(1:27, nrow=3) mz <- 101:103 coord <- expand.grid(x=1:3, y=1:3) msset <- MSImageSet(spectra=spectra, mz=mz, coord=coord) ## Access a single image corresponding to the first feature imageData(msset)[1,,] ## Reconstruct the datacube imageData(msset)[] ## Access the P x N matrix of column-wise mass spectra spectra(msset) ## Subset the MSImageSet to the first 2 m/z values and first 6 mass spectra msset2 <- msset[1:2, 1:6] imageData(msset2)[] msset2