CHANGES IN VERSION 1.2.0 ------------------------ NEW FEATURES o Add 'rowData' argument to SummarizedExperiment() constructor. This allows the user to supply the row data at construction time. o The SummarizedExperiment() constructor function and the assay() setter now both take any matrix-like object as long as the resulting SummarizedExperiment object is valid. o Support r/cbind'ing of SummarizedExperiment objects with assays of arbitrary dimensions (based on a patch by Pete Hickey). o Add "is.unsorted" method for RangedSummarizedExperiment objects. o NULL colnames() supported during SummarizedExperiment construction. o readKallisto() warns early when files need names. o base::rank() gained a new 'ties.method="last"' option and base::order() a new argument ('method') in R 3.3. Thus so do the "rank" and "order" methods for RangedSummarizedExperiment objects. SIGNIFICANT USER-VISIBLE CHANGES o Re-introduce the rowData() accessor (was defunt in BioC 3.2) as an alias for mcols() and make it the preferred way to access the row data. There is now a pleasant symmetry between rowData and colData. o Rename SummarizedExperiment0 class -> SummarizedExperiment. o Improved vignette. o Remove updateObject() method for "old" SummarizedExperiment objects. DEPRECATED AND DEFUNCT o exptData() is now defunct, metadata() should be used instead. BUG FIXES o Fix bug in "sort" method for RangedSummarizedExperiment objects when 'ignore.strand=TRUE' (the argument was ignored). o Fix 2 bugs when r/cbind'ing SummarizedExperiment objects: - r/cbind'ing assays without names would return only the first element. See https://stat.ethz.ch/pipermail/bioc-devel/2015-November/008318.html - r/cbind'ing assays with names in different order would stop() with 'Assays must have the same names()" o Fix validity method for SummarizedExperiment objects reporting incorrect numbers when the nb of cols in assay(x) doesn't match the nb of rows in colData(x). o assay colnames() must agree with colData rownames() o Fix bug where assays(se, withDimnames=TRUE) was dropping the dimnames of the 3rd and higher-order dimensions of the assays. Thanks to Pete Hickey for catching this and providing a patch. o A couple of minor tweaks to the rowData() setter to make it behave consistently with mcols()/elementMetadata() setters for Vector objects in general. CHANGES IN VERSION 0.3.* ------------------------ NEW FEATURES o readKallisto() and readKallistoBootstrap() input kallisto transcript quantification output into SummarizedExperiment (and other) instances.