CoreSet2 {CoreGx}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

CoreSet2(
  name = "emptySet",
  treatment = data.frame(),
  sample = data.frame(),
  molecularProfiles = MultiAssayExperiment(),
  treatmentResponse = LongTable(),
  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. This slot is not implemented for a CoreSet object yet.

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.

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


[Package CoreGx version 1.5.7 Index]