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NEWS.md

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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