- Debugging vignette issues on the Bioconductor build system
- Added new vignette documenting support for drug combination modelling new drug combination features added in PharmacoGx >=3.0
- 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
- Update to slot names "cell" -> "sample" and "drug" -> "treatment"
- Update standardized identifier column names to match the above slot nomenclature: "cellid" -> "sampleid", "drugid" -> "treatmentid"
- 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
- Fix: remove 'fdr' item from geneDrugSensitivity return vector
- Fix: reverted GDSCsmall.rda and CCLEsmall.rda to original data format; they were accidentally pushed with MultiAssayExperiments in @molecularProfiles
- Spring Bioconductor release!
- Added experimental support for a new class, the
LongTable
, for storing the sensitivity data in aPharmacoSet
. - 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 aPharmacoSet
object, converts the data in the@sensitivty
slot to aLongTable
and returns an updatedPharmacoSet
object. - The
LongTable
class will be used in the future to allowPharmacoSet
s to store treatment response experiments with multiple drugs or cell-lines, greatly expanding the variety of data which can be stored in aPharmacoSet
object. - For more details on the
LongTable
class, please see the vignette in theCoreGx
package.
- 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 theSummarizedExperiment
class instead of the theExpressionSet
class- Argument
pSet
in most PharmacoSet accessor methods now converted toobject
instead; this will break code using names parameters for these accessor methods