CHANGES IN VERSION 1.6.1
------------------------

BUG FIXES

    o '$' completion on SummarizedExperiment works in RStudio and on
      RangedSummarizedExperiment.

CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

    o Add saveHDF5SummarizedExperiment() and loadHDF5SummarizedExperiment() for
      saving/loading HDF5-based SummarizedExperiment objects to/from disk.

DEPRECATED AND DEFUNCT

    o Remove SummarizedExperiment0 class (was introduced to ease transition
      from old SummarizedExperiment class defined in GenomicRanges to new
      RangedSummarizedExperiment class defined in SummarizedExperiment package).


CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o Add makeSummarizedExperimentFromDataFrame() function.

    o Add "acbind" and "arbind" methods for Matrix objects.

SIGNIFICANT USER-VISIBLE CHANGES

    o Speed up "cbind" method for SummarizedExperiment objects based on a
      suggestion by Peter Hickey.

DEPRECATED AND DEFUNCT

    o Remove exptData() getter and setter (were defunct in BioC 3.3).

BUG FIXES


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.

