\name{SCEnews}
\title{SingleCellExperiment News}
\encoding{UTF-8}

\section{Version 1.34.0}{\itemize{
\item \code{counts()}, \code{logcounts()} and other named getters/setters will now raise a warning if \code{i=} is specified,
rather than silently treating it as the next argument to \code{assay()} (usually \code{withDimnames=}). 
}}

\section{Version 1.30.0}{\itemize{
\item Preserve NAs in the input matrices to \code{rowPairs()} and \code{colPairs()} converting them to SelfHits. 
}}

\section{Version 1.28.0}{\itemize{
\item Minor optimization to \code{updateObject()} to return early if the object is more recent than the package version.
}}

\section{Version 1.14.0}{\itemize{
\item Added the \code{unsplitAltExps()} function to reverse the effect of splitting alternative experiments.

\item Added a \code{mainExpName()} getter and setter to remember the name of the main experiment.

\item \code{splitAltExps()} will now store the chosen \code{ref} as the \code{mainExpName}.

\item \code{swapAltExp()} now discards the promoted experiment from the list of alternative experiments in the output.
It will also exchange the \code{colData} between the swapped experiments when \code{withColData=TRUE}.
These changes assist in achieving reversibility of the output.

\item Added \code{applySCE()} to conveniently apply a function to the main and alternative Experiments.

\item Added \code{withDimnames=} to \code{reducedDim<-()} and \code{reducedDims<-()}. 
If \code{TRUE}, these methods now emit warnings on observing incompatible row names in \code{value}.

\item Respect any metadata passed in with \code{value} in \code{reducedDims<-()} and \code{altExps<-()}.

\item Added the reduced.dim.matrix class to preserve attributes inside the \code{reducedDims} during subsetting/combining.

\item Setting \code{withColData=TRUE} in \code{altExp()} and \code{altExps()} will now prepend \code{colData(x)} to the output \code{colData}.

\item Added \code{withDimnames=} to \code{altExp<-()} and \code{altExps<-()}. 
If \code{TRUE}, these methods now emit warnings on observing incompatible column names in \code{value}.
Also added \code{withColData=}, which will now reverse the prepending in the getter if the left-most columns are the same as \code{colData(x)}.
(If not the same, a warning is emitted.)
}}

\section{Version 1.12.0}{\itemize{
\item Added the \code{rowSubset()} function as a standard location for a row subset.

\item Added \code{colPairs()} and \code{rowPairs()} to store pairwise information (e.g., for graphs).

\item Added method specifications for \pkg{S4Vectors} compatibility.
}}

\section{Version 1.10.0}{\itemize{
\item Removed deprecated modes for getting and setting \code{reducedDims}.

\item Added the \code{colLabels} function as a standard location for column labels.

\item Added more options to control \code{sizeFactors} behavior when size factors are missing.
}}

\section{Version 1.8.0}{\itemize{
\item Added altExp() and related methods to get and set alternative Experiments.

\item Added the splitAltExps() utility to create many alternative Experiments at once.

\item Added the swapAltExp() utility to swap between main and alternative Experiments.

\item Deprecated isSpike(), spikeNames() and related arguments for handling spike-ins,
in favor of representing spike-ins as alternative Experiments.

\item Deprecated type= in sizeFactors() and sizeFactorNames(), 
which were previously only required to store size factors for spike-ins.

\item Internal change to the representation of reducedDims() to streamline subsetting and combining.
}}

\section{Version 1.4.0}{\itemize{
\item Allow ... arguments to be passed to rowData() and colData().

\item Added weights() methods for getting/setting observational weights.

\item Added reducedDimNames<- method to set the names of reduced dimension slots.

\item Added withDimnames= argument to reducedDim() and reducedDims().

\item Exported getters and setters for internal metadata fields.

\item Added developer instructions for making use of internal metadata fields.
}}

\section{Version 1.2.0}{\itemize{
\item Added the clearSpikes() function to remove all spike-in information.

\item Added the clearSizeFactors() function to remove all size factor information.

\item Added the sizeFactorNames() function to query the available (named) size factor sets.

\item isSpike() with an unknown spike-in set in type= will no longer throw an error, and will quietly return NULL.

\item 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.

\item Added the LinearEmbeddingMatrix class for storing dimensionality reduction with loadings.
}}

\section{Version 1.0.0}{\itemize{
\item
New package SingleCellExperiment, for representation of single-cell genomics data.
}}
