CHANGES IN VERSION 1.28.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o SummarizedExperiment objects now accept NAs in their rownames.
Important notes:
- NAs in the **rownames** are now tolerated but will cause problems
downstream e.g. they break the rowData() getter unless 'use.names=FALSE'
is used.
- NAs in the **colnames** are not and cannot be supported at the moment!
Right now they break the SummarizedExperiment() constructor in an ugly
way (error message not super helpful):
> SummarizedExperiment(m)
Error in DataFrame(x = seq_len(ncol(a1)), row.names = nms) :
missing values in 'row.names'
This will need to be improved.
- At the root of these problems is the fact that at the moment DataFrame
objects do NOT support NAs in their rownames.
Bottom line: NAs in the dimnames of a SummarizedExperiment object should
be avoided at all cost. One way to deal with them is to replace them with
empty strings ("").
See commit 71872cc03b7c0195fb80d1d09409243f049ebb3f.
o Small tweak to combineRows/combineCols: combineRows() and combineCols()
no longer need to "fix" the dimnames that end up on the combined assays
of the returned SummarizedExperiment object. So the assay dimnames are
now returned as-is.
See commit 1d6610eb168330f32433273e4fe49da173dcd33b.
CHANGES IN VERSION 1.26.0
-------------------------
DEPRECATED AND DEFUNCT
o readKallisto() is now defunct after being deprecated in BioC 3.12.
CHANGES IN VERSION 1.24.0
-------------------------
NEW FEATURES
o Add 'checkDimnames' argument to SummarizedExperiment() constructor
function
o Add showAsCell() method for SummarizedExperiment objects.
SIGNIFICANT USER-VISIBLE CHANGES
o Check the assay dimnames at SummarizedExperiment construction time:
The SummarizedExperiment() constructor function now raises an error
if one of the supplied assays has rownames and/or colnames that don't
match those of the SummarizedExperiment object to construct.
CHANGES IN VERSION 1.22.0
-------------------------
NEW FEATURES
o Add combineRows() and combineCols() methods for SummarizedExperiment
objects and derivatives. These are more flexible versions of rbind()
and cbind() that don't require the objects to combine to have the same
columns or rows. Contributed by Aaron Lun.
CHANGES IN VERSION 1.20.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o SummarizedExperiment now depends on the MatrixGenerics package.
o DelayedArray was moved from Depends to Imports.
DEPRECATED AND DEFUNCT
o Deprecated readKallisto().
BUG FIXES
o Avoid triggering copies of the assays in assays() getter.
o Fix long-standing bug in dim() method for Assays objects.
o Fix assays(x) <- SimpleList(). Before that fix this operation was turning
SummarizedExperiment object (or derivative) 'x' into an invalid object.
CHANGES IN VERSION 1.18.0
-------------------------
NEW FEATURES
o SummarizedExperiment objects with assays of > 4 dimensions are now
fully supported.
SIGNIFICANT USER-VISIBLE CHANGES
o By default the assays() and assay() setters now reject inconsistent
dimnames.
By default the dimnames on the supplied assay(s) must be identical to
the dimnames on the SummarizedExperiment object. The user now must use
'withDimnames=FALSE' if it's not the case or they get an error.
This is for symmetry with the behavior of the assays() and assay()
getters (see issue #35). Unfortunately this change is likely to break
existing code but at least the fix is easy.
o dimnames() now returns NULL instead of list(NULL, NULL) on a
SummarizedExperiment object with no dimnames. This is consistent
with matrix objects.
o Swap positions of arguments '...' and 'withDimnames' in assays()
setter and getter. So now it's:
assays(x, withDimnames=TRUE, ...)
assays(x, withDimnames=TRUE, ...) <- value
o Add 'withDimnames' argument to the assay() getter/setter. So now it's:
assay(x, i, withDimnames=TRUE, ...)
assay(x, i, withDimnames=TRUE, ...) <- value
Note that before this change, the user was able to explicitly set
'withDimnames' when calling assay() but since this was not a formal
argument it was forwarded to assays() via the ellipsis. Having it as
a formal argument makes it easier to discover and allows tab completion.
CHANGES IN VERSION 1.16.0
-------------------------
NEW FEATURES
o Some improvements to the SummarizedExperiment() constructor (see commit
0d74843c)
o Support 'colData(SummarizedExperiment) <- NULL' to clear colData
SIGNIFICANT USER-VISIBLE CHANGES
o All the arguments of the SummarizedExperiment() constructor are now
visible (no more ellipsis) and have default values. So tab completion
works. See commit 0d74843c
o The dimnames on the individual assays of a SummarizedExperiment derivative
now can be anything (see issue #25 for the details)
BUG FIXES
o Some fixes to the SummarizedExperiment() constructor (see commit
0d74843c)
o Address all.equal() false positives on SummarizedExperiment objects
(see issue #16 for the details)
CHANGES IN VERSION 1.12.0
-------------------------
NEW FEATURES
o The package has a new vignette "Extending the SummarizedExperiment class"
by Aaron Lun intended for developers. It documents in great details the
process of implementing a SummarizedExperiment extension (a.k.a.
subclass).
SIGNIFICANT USER-VISIBLE CHANGES
o rowData() gains use.names=TRUE argument; prior behavior was to
use.names=FALSE. rowData() by default fails when rownames()
contains NAs.
BUG FIXES
o Better error handling in SummarizedExperiment() constructor.
SummarizedExperiment() now prints an informative error message when
the supplied assays have insane rownames or colnames. This addresses
https://github.com/Bioconductor/SummarizedExperiment/issues/7
CHANGES IN VERSION 1.10.0
-------------------------
NEW FEATURES
o Add "subset" method for SummarizedExperiment objects. See
https://github.com/Bioconductor/SummarizedExperiment/pull/6
o rowRanges() now is supported on a SummarizedExperiment object that is
not a RangedSummarizedExperiment, and returns NULL. Also doing
'rowRanges(x) <- NULL' on a RangedSummarizedExperiment object now is
supported and degrades it to a SummarizedExperiment instance.
o Add 'BACKEND' argument to "realize" method for SummarizedExperiment
objects.
SIGNIFICANT USER-VISIBLE CHANGES
o saveHDF5SummarizedExperiment() and loadHDF5SummarizedExperiment() are
now in the HDF5Array package.
o Replace old "updateObject" method for SummarizedExperiment objects with
a new one.
The new method calls updateObject() on all the assays of the object.
This will update SummarizedExperiment objects (and their derivatives
like BSseq objects) that have "old" DelayedArray objects in their assays.
The old method has been around since BioC 3.2 (released 2.5 years ago)
and was used to update objects made prior to the change of internals
that happened between BioC 3.1 and BioC 3.2. All these "old" objects
should have been updated by now so we don't need this anymore.
BUG FIXES
o Modify the "[<-" method for SummarizedExperiment to leave 'metadata(x)'
intact instead of trying to combine it with 'metadata(value)'. With this
change 'x[i , j] <- x[i , j]' behaves like a no-op (as expected) instead
of duplicating metadata(x).
o The SummarizedExperiment() constructor does not try to downgrade the
supplied rowData and/or colData to DataFrame anymore if they derive
from DataFrame.
CHANGES IN VERSION 1.8.0
------------------------
NEW FEATURES
o Add 'chunk_dim' and 'level' arguments to saveHDF5SummarizedExperiment().
o Add coercion from ExpressionSet to SummarizedExperiment.
DEPRECATED AND DEFUNCT
o Remove 'force' argument from seqinfo() and seqlevels() setters (the
argument got deprecated in BioC 3.5 in favor of new and more flexible
'pruning.mode' argument).
BUG FIXES
o Coercion from SummarizedExperiment to RangedSummarizedExperiment was
losing the metadata columns. Fixed now.
o Fix cbind() and rbind() of SummarizedExperiment objects when some of the
assays are DataFrame or data.frame objects.
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.