NEWS.md

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

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 PharmacoSets 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

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.