NEWS

CoreGx 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

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)

Add error message to CoreSet,show-method which lets users know to use updateObject if the slot names are not valid

Add endoaggregate method to compute TreatmentResponseExperiment assay aggregations within the object
Add mergeAssays method to allow joining assaying within a TreatmentResponseExperiment

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.

Fix bug in logLogisticRegression causing tests to fail in Bioconductor 3.16 daily builds

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

Fixed imports for the CoreSet2 constructor to resolve errors in downstream package PharmacoGx

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!

Fix bug in LongTable -> data.table coerce method that was causing rows of some assays to be dropped (closes issue #)

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

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

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

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.

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

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

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.

Bug fix: suppress warnings thrown by piano::runGSA inside the connectivitScore function

Updated the CoreGx vignette to include more information on extending the CoreSet class for use in other treatment-response experiments.

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