iSet contain one or more arrays or array-like objects with an equal number of dimensions as imageData elements. It is assumed that the first dimension of each such element corresponds to the data features, and all other dimensions are described by associated coordinates in the pixelData slot. Otherwise, derived classes are responsible for managing how the elements of imageData behave and their relationship with the rows of pixelData and featureData. The MSImageSet class for mass spectrometry imaging experiments is the primary derived class of iSet. Its parent class SImageSet is another derived class for more general images.
This class is based on the eSet virtual class from Biobase. However, the iSet class contains an imageData slot which is an 'immutableEnvironment' that preserves copy-on-write behavior for iSet derived classes, but only copying elements of imageData when that slot specifically is modified. In addition pixelData is an IAnnotatedDataFrame that stores pixel information such as pixel coordinates in addition to phenotypic data.
imageData:ImageData, which stores one or more array or array-like objects 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:IAnnotatedDataFrame. This includes both pixel coordinates and phenotypic and sample data. Its rows correspond to individual pixels, many of which may belong to the same sample. Apart a requirement on columns describing the pixel coordinates, it is left to derived classes to decide the relationship to elements of imageData.featureData:imageData.experimentData:MIAxE.protocolData:pixelData..__classVersion__:Versions object describing the version of the class used to created the instance. Intended for developer use.VersionedBiobase, directly.
Versioned, by class "VersionedBiobase", distance 2.iSet is a virtual class. No instances can be created.sampleNames(object), sampleNames(object) <- value:pixelData and protocolData slots.featureNames(object), featureNames(object) <- value:featureData slot.pixelNames(object), pixelNames(object) <- value:pixelData slot.coordLabels(object), coordLabels(object) <- value:pixelData slot. Note that this does not set or get coordinate names with a labelType of sample, regardless of whether they are currently being used to describe coordinates or not. Therefore, checking coordLabels(object) versus names(coord(object)) is a simple way of checking whether a dataset is 2D or 3D.coord(object), coord(object)<-:data.frame containing the subset of columns of data for which the variables have a 'labelType' of 'dim'.imageData(object), imageData(object) <- value:imageData slot.pixelData(object), pixelData(object) <- value:pixelData slot.pData(object), pData(object) <- value:varMetadata(object), varMetadata(object) <- value:pData.varLabels(object), varLabels(object) <- value:pixelData.featureData(object), featureData(object) <- value:featureData slot.fData(object), fData(object) <- value:fvarMetadata(object), fvarMetadata(object) <- value:fData.fvarLabels(object), fvarLabels(object) <- value:featureData.features(object, ...):featureData) corresponding to variables in featureData.pixels(object, ...):pixelData) corresponding to variables in pixelData.experimentData(object), experimentData(object) <-:experimentData slot.protocolData(object), protocolData(object) <-:protocolData slot.storageMode(object), storageMode(object)<-:imageData slot. See documentation on the storageMode slot above for more details.initialize:iSet derived class. Called by new. Not to be used by the user.validObject:pixelData describing the pixel coordinates, cooresponding to the dimensions of the elements of imageData. For every named dimension of the arrays on imageData there must be a pData column describing its pixel coordinates. Also checks that the sampleNames match between pixelData and protocolData.combine(x, y, ...):iSet objects. To be combined, iSets must have identical featureData and distinct pixelNames and sampleNames. All elements of imageData must have matching names. Elements of imageData are combined by calls for combine.dim:dims(object) (which corresponds to the arrays in data) or returned by dim(imageData(object)). See SImageSet for an example where this is the case, due to its use of a "virtual" datacube.dims:data slot.iSet$name, iSet$name <- value:name column in pixelData.iSet[[i, ...]], iSet[[i, ...]] <- value:i (character or numeric index) in pixelData. The ... argument can include named variables (especially 'labelDescription') to be added to the varMetadata.eSet,
SImageSet,
MSImageSet
## Cannot create an iSet object
try(new("iSet"))
## Create an iSet derived class
MyImageSet <- setClass("MyImageSet", contains="iSet")
MyImageSet()
removeClass("MyImageSet")
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