# Package Release News # 3.3.2 - Debugging vignette issues on the Bioconductor build system # 3.3.1 - Added new vignette documenting support for drug combination modelling new drug combination features added in PharmacoGx >=3.0 # 3.1.4 - Modified downloadPSet function to automatically update the PharmacoSet class structure and resave the updated object after download - This work around is necessary until we can rerun our data engineering pipelines to regenerate all of our PharmacoSet using the 3.1.0 package updates - Added a number of additional methods for computing drug synergy metrics # 3.1.1 ## 3.1.0 - Update to slot names "cell" -> "sample" and "drug" -> "treatment" - Update standardized identifier column names to match the above slot nomenclature: "cellid" -> "sampleid", "drugid" -> "treatmentid" # 2.5 ## 2.5.3 - Added PharmacoSet2 constructor to allow creation of PSets with updated class definition introducted in BioC 3.13 - The sensitivity slot is now required to be a TreatmentResponseExperiment - The molecularProfiles slot is now required to be a MultiAssayExperiment - The original constructor and all accessors remain in the package for full backwards compatibility ## v2.5.2 - Fix: remove 'fdr' item from geneDrugSensitivity return vector ## v2.5.1 - Fix: reverted GDSCsmall.rda and CCLEsmall.rda to original data format; they were accidentally pushed with MultiAssayExperiments in @molecularProfiles ## v2.5.0 - Spring Bioconductor release! ## v2.1.12 - Added experimental support for a new class, the `LongTable`, for storing the sensitivity data in a `PharmacoSet`. - Because this is not well tested, we have left not updated the PSets available via the `downloadPSets` function. - Instead we have provided a convenient function, `convertSensitivitySlotToLongTable`, which takes in a `PharmacoSet` object, converts the data in the `@sensitivty` slot to a `LongTable` and returns an updated `PharmacoSet` object. - The `LongTable` class will be used in the future to allow `PharmacoSet`s to store treatment response experiments with multiple drugs or cell-lines, greatly expanding the variety of data which can be stored in a `PharmacoSet` object. - For more details on the `LongTable` class, please see the vignette in the `CoreGx` package. ## v2.0.0 - PharmacoGx now depends on CoreGx, a package designed to abstract core functionality from PharmacoGx for use in other Gx suite packages - `PharmacoSet` class has been modified to store molecular profile data in the `SummarizedExperiment` class instead of the the `ExpressionSet` class - Argument `pSet` in most PharmacoSet accessor methods now converted to `object` instead; this will break code using names parameters for these accessor methods