PharmacoSet2 {PharmacoGx}

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(),
  curation = list(sample = data.frame(), treatment = data.frame(), tissue =
    data.frame())
)

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.
curation	This class requires an additional curation item, tissue, which maps from published to standardized tissue idenifiers.

Value

A CoreSet object storing standardized and curated treatment response and multiomic profile data associated with a given publication.

Examples

data(CCLEsmall)
CCLEsmall

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