Changes in version 2.1.7
- Fixed a bug when deleting a TreatmentResponseExperiment assay via
NULL assignment
- Added a names S4 method fo TreatmentResponseExperiment to enable tab
autocomplete with $ access in interative sessions
- Added additional methods for drug combination modelling; these
changes will be documented in a new vignette once we have thoroughly
tested the new functions
- For now these are experimental and should not be considered a
stable API
Changes in version 2.1.6
- Changed default parallelization strategy inside aggregate2 (and
therefore inside aggregate,TreatmentResponseExperiment-method and
endoaggregate) to split the table into nthread tables instead of
using by
- Result should be (1) parallelization is now always faster than
serial computations, which was not true previously
- Memory usage of parallelization should be much smaller, since we
aren't splitting into a very long list of tables
- Optimized the internal representation of the
TreatmentResponseExperiment assay index to remove storage of NA for
rowKey-colKey combinations with no observations in any assay
- This was causing memory usage to baloon if both rowKey and
colKey were a large sequence
- Prepended a "." to the internal assay index column names for each
assay
- This should reduce name clashes between internal TRE metadata
and the column names of an assay (specifically, you can now have
a column with the same name as the assay)
Changes in version 2.1.5
- Add error message to CoreSet,show-method which lets users know to
use updateObject if the slot names are not valid
Changes in version 2.1.4
- Add endoaggregate method to compute TreatmentResponseExperiment
assay aggregations within the object
- Add mergeAssays method to allow joining assaying within a
TreatmentResponseExperiment
Changes in version 2.1.3
- Updated CoreSet vignette to reflect recent changes to the object
structure
- Renamed the LongTable vignette to TreatmentResponseExperiment and
updated the content to reflect the changes in class structure
from 2.1.1
- Generated new TreatmentResponseExperiment class and structure
diagrams and inlcuded them in the TreamentResponseExperiment
vignette
- Added new example TreatmentResponseExperiment object to package data
- Added various unit tests for the LongTable (and therefore also the
TreatmentResponseExperiment)
- Added proper documentation object for the TREDataMapper-accessors
- Added aggregate methods for data.table and LongTable
- Added endoaggregate method for LongTable, which uses aggregate
internally but assigns the result back to the object and returns the
updated object. Thus this method is an endomorphic version of
aggregate.
- Added new argument summarize to assay,LongTable-method which only
attaches columns which have been summarized over if FALSE
- Added assayCols and assayKeys helper methods to retrive valid assay
column names or the key columns for an assay, respectively.
Changes in version 2.1.2
- Fix bug in logLogisticRegression causing tests to fail in
Bioconductor 3.16 daily builds
Changes in version 2.1.1
- First update since Bioconductor 3.15 release
- Merged rework of the LongTable class back into main branch
- The object has now been updated to
Changes in version 2.0.0
- The @cell slot has become the @sample slot. Associated generics and
accessor methods have been renamed, then aliased to their old names.
As such, old code should still work as expected, but will in fact be
calling different S4 methods.
- Added the @treatment slot to the CoreSet-class
- Renamed @sensitivity slot to @treatmentResponse
Changes in version 1.5.8
- Fixed imports for the CoreSet2 constructor to resolve errors in
downstream package PharmacoGx
Changes in version 1.5.7
- Add TreatmentResponseExperiment class, a simple wrapper around
LongTable to make the class syntax more domain specific
- Add CoreSet2 structure to support creation of CoreSets with the
modified class structure introducted in BioC 3.13
- CoreSets can now be made with treatment combination experiments via
the TreatmentResponseExperiment class!
Changes in version 1.5.6
- Fix bug in LongTable -> data.table coerce method that was causing
rows of some assays to be dropped (closes issue #)
Changes in version 1.5.5
- Fix bug in .distancePointLine where function fails with no intercept
specified (Issue #120)
- Added support for aggregating an assay inside of a LongTable class
object
- Some in-progress updates to the CoreSet constructor which will be
completed for the Fall release
- Fixed an error in treatmentNames example
- Fixed roxygen2 documentation warnings about S4 method documentation
- Overhauled LongTable coerce methods to use the LongTableDataMapper
class instead of the deprecated 'LongTable.config' attribute
Changes in version 1.5.4
- Fix bug in $<- and [[<- methods where value was returned instead of
updated object
- Fix bug in .sanitize input caused by length > 1 coercing to logical
vector
Changes in version 1.5.3
- Fix bug in connectivityScore caused by length > 1 coercing to
logical vector; this should fix errors in RadioGx and PharmacoGx
vignettes that were caused by failed R CMD build
Changes in version 1.5.2
- Add subsetBySample method for CoreSet object; this is the first step
in modularizing the subset methods for reuse in dependent packages
- Added a CoreSet-utils documentation section to document subset,
intersect, combine and other set operations for a CoreSet object.
Changes in version 1.5.1
- Fixed some spelling errors and incorrect code chunk configurations
in the LongTable vignette
- Fix bug in .rebuildProfiles where the function fails if replicate_id
is assigned as a rowID column in the LongTable in @sensitivity
Changes in version 1.5.0
- Bioconductor spring 2021 release
- Added the DataMapper abstract class
- Added the LongTableDataMapper concrete class
- Added the metaConstruct method, for making an S4 object from a
sub-class of DataMapper
- Updated LongTable vignette with documentation for the DataMapper and
LongTableDataMapper
- Refactored various methods to work with a LongTable in @sensititivty
- Refactored various methods to work with a MultiAssayExperiment in
@molecularProfiles
Changes in version 1.1.5
- Implemented a new class, the LongTable, to store the results of a
treatment response experiment. This class provides a flexible and
fast data storage object which can be subclassed for use in other R
packages.
- Added vignette documenting LongTable accessors and usage of the new
object.
Changes in version 1.0.2
- Bug fix: suppress warnings thrown by piano::runGSA inside the
connectivitScore function
Changes in version 1.0.1
- Updated the CoreGx vignette to include more information on extending
the CoreSet class for use in other treatment-response experiments.
Changes in version 1.0.0
- Implemented molecularProfiles as SummarizedExperiments instead of
ExpressionSets
- Modifying generic implementation to add ...; allows for additional
arguments in setMethods() for CoreGx generics
- Removing package from CRAN
- Submitting package to Bioconductor