/usr/lib/R/site-library/SummarizedExperiment/NEWS is in r-bioc-summarizedexperiment 1.4.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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
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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.*
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NEW FEATURES
o readKallisto() and readKallistoBootstrap() input kallisto
transcript quantification output into SummarizedExperiment (and
other) instances.
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