Changes in version 1.14.0
o Added the unsplitAltExps() function to reverse the effect of
splitting alternative experiments.
o Added a mainExpName() getter and setter to remember the name of
the main experiment.
o splitAltExps() will now store the chosen ref as the
mainExpName.
o 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.
o Added applySCE() to conveniently apply a function to the main
and alternative Experiments.
o Added withDimnames= to reducedDim<-() and reducedDims<-(). If
TRUE, these methods now emit warnings on observing incompatible
row names in value.
o Respect any metadata passed in with value in reducedDims<-()
and altExps<-().
o Added the reduced.dim.matrix class to preserve attributes
inside the reducedDims during subsetting/combining.
o Setting withColData=TRUE in altExp() and altExps() will now
prepend colData(x) to the output colData.
o 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.)
Changes in version 1.12.0
o Added the rowSubset() function as a standard location for a row
subset.
o Added colPairs() and rowPairs() to store pairwise information
(e.g., for graphs).
o Added method specifications for S4Vectors compatibility.
Changes in version 1.10.0
o Removed deprecated modes for getting and setting reducedDims.
o Added the colLabels function as a standard location for column
labels.
o Added more options to control sizeFactors behavior when size
factors are missing.
Changes in version 1.8.0
o Added altExp() and related methods to get and set alternative
Experiments.
o Added the splitAltExps() utility to create many alternative
Experiments at once.
o Added the swapAltExp() utility to swap between main and
alternative Experiments.
o Deprecated isSpike(), spikeNames() and related arguments for
handling spike-ins, in favor of representing spike-ins as
alternative Experiments.
o Deprecated type= in sizeFactors() and sizeFactorNames(), which
were previously only required to store size factors for
spike-ins.
o Internal change to the representation of reducedDims() to
streamline subsetting and combining.
Changes in version 1.4.0
o Allow ... arguments to be passed to rowData() and colData().
o Added weights() methods for getting/setting observational
weights.
o Added reducedDimNames<- method to set the names of reduced
dimension slots.
o Added withDimnames= argument to reducedDim() and reducedDims().
o Exported getters and setters for internal metadata fields.
o Added developer instructions for making use of internal
metadata fields.
Changes in version 1.2.0
o Added the clearSpikes() function to remove all spike-in
information.
o Added the clearSizeFactors() function to remove all size factor
information.
o Added the sizeFactorNames() function to query the available
(named) size factor sets.
o isSpike() with an unknown spike-in set in type= will no longer
throw an error, and will quietly return NULL.
o 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.
o Added the LinearEmbeddingMatrix class for storing
dimensionality reduction with loadings.
Changes in version 1.0.0
o
New package SingleCellExperiment, for representation of
single-cell genomics data.