Version: 1.42.0 Text: No significant changes in this version. Version: 1.40.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Depends on the new Seqinfo package instead of GenomeInfoDb. Version: 1.38.0 Text: No changes in this version. Version: 1.36.0 Category: NEW FEATURES Text: Calling saveRDS() on a SummarizedExperiment object that contains out-of-memory data now raises an error with a message that redirects the user to HDF5Array::saveHDF5SummarizedExperiment(). Version: 1.36.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Move documentation of constructor function SummarizedExperiment() from RangedSummarizedExperiment-class.Rd to SummarizedExperiment-class.Rd. See https://github.com/Bioconductor/SummarizedExperiment/issues/80 Version: 1.36.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Change default value of 'rowData' argument in SummarizedExperiment() constructor from GRangesList() to NULL. Version: 1.36.0 Category: BUG FIXES Text: Fix typos in error message from assay() and assays() setters. Version: 1.34.0 Category: NEW FEATURES Text: Add terminators() method, same as promoters() but for terminator regions. Version: 1.34.0 Category: NEW FEATURES Text: Add "Top-level dimnames vs assay-level dimnames" section to vignette. Also fix typo in man/SummarizedExperiment-class.Rd. This is in response to https://github.com/Bioconductor/SummarizedExperiment/issues/79 Version: 1.34.0 Category: BUG FIXES Text: Fix typo in man/SummarizedExperiment-class.Rd Version: 1.32.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Vignette gains a new section about interactive visualization with iSEE. Version: 1.30.0 Category: DEPRECATED AND DEFUNCT Text: Finally remove readKallisto() (got deprecated in BioC 3.12 and defunct in BioC 3.15). Version: 1.28.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.28.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.26.0 Category: DEPRECATED AND DEFUNCT Text: readKallisto() is now defunct after being deprecated in BioC 3.12. Version: 1.24.0 Category: NEW FEATURES Text: Add 'checkDimnames' argument to SummarizedExperiment() constructor function Version: 1.24.0 Category: NEW FEATURES Text: Add showAsCell() method for SummarizedExperiment objects. Version: 1.24.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.22.0 Category: NEW FEATURES Text: 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. Version: 1.20.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: SummarizedExperiment now depends on the MatrixGenerics package. Version: 1.20.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: DelayedArray was moved from Depends to Imports. Version: 1.20.0 Category: DEPRECATED AND DEFUNCT Text: Deprecated readKallisto(). Version: 1.20.0 Category: BUG FIXES Text: Avoid triggering copies of the assays in assays() getter. Version: 1.20.0 Category: BUG FIXES Text: Fix long-standing bug in dim() method for Assays objects. Version: 1.20.0 Category: BUG FIXES Text: Fix assays(x) <- SimpleList(). Before that fix this operation was turning SummarizedExperiment object (or derivative) 'x' into an invalid object. Version: 1.18.0 Category: NEW FEATURES Text: SummarizedExperiment objects with assays of > 4 dimensions are now fully supported. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: dimnames() now returns NULL instead of list(NULL, NULL) on a SummarizedExperiment object with no dimnames. This is consistent with matrix objects. Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Swap positions of arguments '...' and 'withDimnames' in assays() setter and getter. So now it's: assays(x, withDimnames=TRUE, ...) assays(x, withDimnames=TRUE, ...) <- value Version: 1.18.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.16.0 Category: NEW FEATURES Text: Some improvements to the SummarizedExperiment() constructor (see commit 0d74843c) Version: 1.16.0 Category: NEW FEATURES Text: Support 'colData(SummarizedExperiment) <- NULL' to clear colData Version: 1.16.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: All the arguments of the SummarizedExperiment() constructor are now visible (no more ellipsis) and have default values. So tab completion works. See commit 0d74843c Version: 1.16.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: The dimnames on the individual assays of a SummarizedExperiment derivative now can be anything (see issue #25 for the details) Version: 1.16.0 Category: BUG FIXES Text: Some fixes to the SummarizedExperiment() constructor (see commit 0d74843c) Version: 1.16.0 Category: BUG FIXES Text: Address all.equal() false positives on SummarizedExperiment objects (see issue #16 for the details) Version: 1.12.0 Category: NEW FEATURES Text: 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). Version: 1.12.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: rowData() gains use.names=TRUE argument; prior behavior was to use.names=FALSE. rowData() by default fails when rownames() contains NAs. Version: 1.12.0 Category: BUG FIXES Text: 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 Version: 1.10.0 Category: NEW FEATURES Text: Add "subset" method for SummarizedExperiment objects. See https://github.com/Bioconductor/SummarizedExperiment/pull/6 Version: 1.10.0 Category: NEW FEATURES Text: 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. Version: 1.10.0 Category: NEW FEATURES Text: Add 'BACKEND' argument to "realize" method for SummarizedExperiment objects. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: saveHDF5SummarizedExperiment() and loadHDF5SummarizedExperiment() are now in the HDF5Array package. Version: 1.10.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.10.0 Category: BUG FIXES Text: 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). Version: 1.10.0 Category: BUG FIXES Text: The SummarizedExperiment() constructor does not try to downgrade the supplied rowData and/or colData to DataFrame anymore if they derive from DataFrame. Version: 1.8.0 Category: NEW FEATURES Text: Add 'chunk_dim' and 'level' arguments to saveHDF5SummarizedExperiment(). Version: 1.8.0 Category: NEW FEATURES Text: Add coercion from ExpressionSet to SummarizedExperiment. Version: 1.8.0 Category: DEPRECATED AND DEFUNCT Text: 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). Version: 1.8.0 Category: BUG FIXES Text: Coercion from SummarizedExperiment to RangedSummarizedExperiment was losing the metadata columns. Fixed now. Version: 1.8.0 Category: BUG FIXES Text: Fix cbind() and rbind() of SummarizedExperiment objects when some of the assays are DataFrame or data.frame objects. Version: 1.8.0 Category: BUG FIXES Text: '$' completion on SummarizedExperiment works in RStudio and on RangedSummarizedExperiment. Version: 1.6.0 Category: NEW FEATURES Text: Add saveHDF5SummarizedExperiment() and loadHDF5SummarizedExperiment() for saving/loading HDF5-based SummarizedExperiment objects to/from disk. Version: 1.6.0 Category: DEPRECATED AND DEFUNCT Text: Remove SummarizedExperiment0 class (was introduced to ease transition from old SummarizedExperiment class defined in GenomicRanges to new RangedSummarizedExperiment class defined in SummarizedExperiment package). Version: 1.4.0 Category: NEW FEATURES Text: Add makeSummarizedExperimentFromDataFrame() function. Version: 1.4.0 Category: NEW FEATURES Text: Add "acbind" and "arbind" methods for Matrix objects. Version: 1.4.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Speed up "cbind" method for SummarizedExperiment objects based on a suggestion by Peter Hickey. Version: 1.4.0 Category: DEPRECATED AND DEFUNCT Text: Remove exptData() getter and setter (were defunct in BioC 3.3). Version: 1.4.0 Category: BUG FIXES Text: Version: 1.2.0 Category: NEW FEATURES Text: Add 'rowData' argument to SummarizedExperiment() constructor. This allows the user to supply the row data at construction time. Version: 1.2.0 Category: NEW FEATURES Text: The SummarizedExperiment() constructor function and the assay() setter now both take any matrix-like object as long as the resulting SummarizedExperiment object is valid. Version: 1.2.0 Category: NEW FEATURES Text: Support r/cbind'ing of SummarizedExperiment objects with assays of arbitrary dimensions (based on a patch by Pete Hickey). Version: 1.2.0 Category: NEW FEATURES Text: Add "is.unsorted" method for RangedSummarizedExperiment objects. Version: 1.2.0 Category: NEW FEATURES Text: NULL colnames() supported during SummarizedExperiment construction. Version: 1.2.0 Category: NEW FEATURES Text: readKallisto() warns early when files need names. Version: 1.2.0 Category: NEW FEATURES Text: 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. Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: 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. Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Rename SummarizedExperiment0 class -> SummarizedExperiment. Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Improved vignette. Version: 1.2.0 Category: SIGNIFICANT USER-VISIBLE CHANGES Text: Remove updateObject() method for "old" SummarizedExperiment objects. Version: 1.2.0 Category: DEPRECATED AND DEFUNCT Text: exptData() is now defunct, metadata() should be used instead. Version: 1.2.0 Category: BUG FIXES Text: Fix bug in "sort" method for RangedSummarizedExperiment objects when 'ignore.strand=TRUE' (the argument was ignored). Version: 1.2.0 Category: BUG FIXES Text: 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()" Version: 1.2.0 Category: BUG FIXES Text: 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). Version: 1.2.0 Category: BUG FIXES Text: assay colnames() must agree with colData rownames() Version: 1.2.0 Category: BUG FIXES Text: 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. Version: 1.2.0 Category: BUG FIXES Text: A couple of minor tweaks to the rowData() setter to make it behave consistently with mcols()/elementMetadata() setters for Vector objects in general. Version: 0.3 Category: NEW FEATURES Text: readKallisto() and readKallistoBootstrap() input kallisto transcript quantification output into SummarizedExperiment (and other) instances.