CoreSet2: Make a CoreSet with the updated class structure

In bhklab/CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

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

CoreSet2(
  name = "emptySet",
  treatment = data.frame(),
  sample = data.frame(),
  molecularProfiles = MultiAssayExperiment(),
  treatmentResponse = LongTable(),
  datasetType = "sensitivity",
  perturbation = list(n = array(dim = 3), info = "No perturbation data!"),
  curation = list(sample = data.frame(), treatment = data.frame())
)

Arguments

name	A character(1) vector with the CoreSet objects name.
treatment	A data.frame with treatment level metadata.
sample	A data.frame with sample level metadata for the union of samples in treatmentResponse and molecularProfiles.
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 CoreSet object.
datasetType	A deprecated slot in a CoreSet object included for backwards compatibility. This may be removed in future releases.
perturbation	A deprecated slot in a CoreSet object included for backwards compatibility. This may be removed in future releases.
curation	A list(2) object with two items named treatment and sample with mappings from publication identifiers to standardized identifiers for both annotations, respectively.

Value

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

Examples

data(clevelandSmall_cSet)
clevelandSmall_cSet

bhklab/CoreGx documentation built on March 14, 2024, 3:04 a.m.