CoreSet constructor

A constructor that simplifies the process of creating CoreSets, as well as creates empty objects for data not provided to the constructor. Only objects returned by this constructor are expected to work with the CoreSet methods.

Usage

CoreSet(
  name,
  molecularProfiles = list(),
  sample = data.frame(),
  sensitivityInfo = data.frame(),
  sensitivityRaw = array(dim = c(0, 0, 0)),
  sensitivityProfiles = matrix(),
  sensitivityN = matrix(nrow = 0, ncol = 0),
  perturbationN = array(NA, dim = c(0, 0, 0)),
  curationSample = data.frame(),
  curationTissue = data.frame(),
  curationTreatment = data.frame(),
  treatment = data.frame(),
  datasetType = c("sensitivity", "perturbation", "both"),
  verify = TRUE,
  ...
)

Arguments

name

A character string detailing the name of the dataset

molecularProfiles

A list of SummarizedExperiment objects containing molecular profiles for each molecular data type.

sample

A data.frame containing the annotations for all the sample profiled in the data set, across all data types. Must contain the mandatory sampleid column which uniquely identifies each sample in the object.

sensitivityInfo

A data.frame containing the information for the sensitivity experiments. Must contain a 'sampleid' column with unique identifiers to each sample, matching the sample object and a 'treatmentid' columns with unique indenifiers for each treatment, matching the treatment object.

sensitivityRaw

A 3 Dimensional array contaning the raw drug dose response data for the sensitivity experiments

sensitivityProfiles

data.frame containing drug sensitivity profile statistics such as IC50 and AUC

sensitivityN, perturbationN

A data.frame summarizing the available sensitivity/perturbation data

curationSample, curationTissue, curationTreatment

A data.frame mapping the names for samples, tissues and treatments used in the data set to universal identifiers used between different CoreSet objects

treatment

A data.frame containing annotations for all treatments profiled in the dataset. Must contain the mandatory treatmentid column which uniquely identifies each treatment in the object.

datasetType

A character(1) string of 'sensitivity', 'preturbation', or 'both' detailing what type of data can be found in the CoreSet, for proper processing of the data

verify

logical(1)Should the function verify the CoreSet and print out any errors it finds after construction?

...

Catch and parse any renamed constructor arguments.

Value

An object of class CoreSet

Details

WARNING:

Parameters to this function have been renamed!

• cell is now sample

• drug is now treatment

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