Added the unsplitAltExps() function to reverse the effect of splitting alternative experiments.
Added a mainExpName() getter and setter to remember the name of the main experiment.
splitAltExps() will now store the chosen ref as the mainExpName.
swapAltExp() now discards the promoted experiment from the list of alternative experiments in the output.
It will also exchange the colData between the swapped experiments when withColData=TRUE.
These changes assist in achieving reversibility of the output.
Added applySCE() to conveniently apply a function to the main and alternative Experiments.
Added withDimnames= to reducedDim<-() and reducedDims<-().
If TRUE, these methods now emit warnings on observing incompatible row names in value.
Respect any metadata passed in with value in reducedDims<-() and altExps<-().
Added the reduced.dim.matrix class to preserve attributes inside the reducedDims during subsetting/combining.
Setting withColData=TRUE in altExp() and altExps() will now prepend colData(x) to the output colData.
Added withDimnames= to altExp<-() and altExps<-().
If TRUE, these methods now emit warnings on observing incompatible column names in value.
Also added withColData=, which will now reverse the prepending in the getter if the left-most columns are the same as colData(x).
(If not the same, a warning is emitted.)
Added the rowSubset() function as a standard location for a row subset.
Added colPairs() and rowPairs() to store pairwise information (e.g., for graphs).
Added method specifications for S4Vectors compatibility.
Removed deprecated modes for getting and setting reducedDims.
Added the colLabels function as a standard location for column labels.
Added more options to control sizeFactors behavior when size factors are missing.
Added altExp() and related methods to get and set alternative Experiments.
Added the splitAltExps() utility to create many alternative Experiments at once.
Added the swapAltExp() utility to swap between main and alternative Experiments.
Deprecated isSpike(), spikeNames() and related arguments for handling spike-ins, in favor of representing spike-ins as alternative Experiments.
Deprecated type= in sizeFactors() and sizeFactorNames(), which were previously only required to store size factors for spike-ins.
Internal change to the representation of reducedDims() to streamline subsetting and combining.
Allow ... arguments to be passed to rowData() and colData().
Added weights() methods for getting/setting observational weights.
Added reducedDimNames<- method to set the names of reduced dimension slots.
Added withDimnames= argument to reducedDim() and reducedDims().
Exported getters and setters for internal metadata fields.
Added developer instructions for making use of internal metadata fields.
Added the clearSpikes() function to remove all spike-in information.
Added the clearSizeFactors() function to remove all size factor information.
Added the sizeFactorNames() function to query the available (named) size factor sets.
isSpike() with an unknown spike-in set in type= will no longer throw an error, and will quietly return NULL.
isSpike<- with type=NULL is deprecated in favour of clearSpikes() for removing existing spike-in information. All spike-in sets must also be explicitly named during assignment.
Added the LinearEmbeddingMatrix class for storing dimensionality reduction with loadings.
New package SingleCellExperiment, for representation of single-cell genomics data.