PharmacoSet2: Make a CoreSet with the updated class structure
In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

PharmacoSet2

R Documentation

Make a CoreSet with the updated class structure

Description

New implementation of the CoreSet constructor to support MAE and TRE. This constructor will be swapped with the original CoreSet constructor as part of an overhaul of the CoreSet class structure.

Usage

PharmacoSet2(
  name = "emptySet",
  treatment = data.frame(),
  sample = data.frame(),
  molecularProfiles = MultiAssayExperiment(),
  treatmentResponse = TreatmentResponseExperiment(),
  perturbation = list(),
  curation = list(sample = data.frame(), treatment = data.frame(), tissue = data.frame()),
  datasetType = "sensitivity"
)

Arguments

`name`	A `character(1)` vector with the `PharmacoSet` objects name.
`treatment`	A `data.frame` with treatment level metadata. Treatments in a `PharmacoSet` represent pharmaceutical compounds.
`sample`	A `data.frame` with sample level metadata for the union of samples in `treatmentResponse` and `molecularProfiles`. Samples in a `PharmacoSet` represent cancer cell-lines.
`molecularProfiles`	A `MultiAssayExperiment` containing one `SummarizedExperiment` object for each molecular data type.
`treatmentResponse`	A `LongTable` or `LongTableDataMapper` object containing all treatment response data associated with the `PharmacoSet` object.
`perturbation`	A deprecated slot in a `PharmacoSet` object included for backwards compatibility. This may be removed in future releases.
`curation`	This class requires an additional curation item, tissue, which maps from published to standardized tissue idenifiers.
`datasetType`	A deprecated slot in a `PharmacoSet` object included for backwards compatibility. This may be removed in future releases.