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Make a CoreSet with the updated class structure

CoreSet2.Rd

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
#> <CoreSet>
#> Name: Cleveland 
#> Date Created: Sat Feb 18 15:10:56 2023 
#> Number of samples:  10 
#> Molecular profiles: <MultiAssayExperiment> 
#>    ExperimentList class object of length 2: 
#>     [1] rna : SummarizedExperiment with 1000 rows and 9 columns 
#>     [2] rnaseq : SummarizedExperiment with 1000 rows and 9 columns 
#> Treatment response: <TreatmentResponseExperiment> 
#>    dim:  9 10 
#>    assays(2): sensitivity profiles 
#>    rownames(9): radiation:1:1 radiation:1:2 ... radiation:8:1 radiation:10:1 
#>    rowData(3): treatment1id treatment1dose replicate_id 
#>    colnames(10): CHP-212 IMR-32 KP-N-S19s ... SK-N-SH SNU-245 SNU-869 
#>    colData(2): sampleid rn 
#>    metadata(1): experiment_metadata