ToxicoSet: ToxicoSet constructor
In bhklab/ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

ToxicoSet

R Documentation

ToxicoSet constructor

Description

A constructor that simplifies the process of creating ToxicoSets, 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 ToxicoSet methods. For a much more detailed instruction on creating ToxicoSets, please see the "CreatingToxicoSet" vignette.

Usage

ToxicoSet(
  name,
  molecularProfiles = list(),
  sample = data.frame(),
  treatment = 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)),
  curationTreatment = data.frame(),
  curationSample = data.frame(),
  curationTissue = 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.
`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.
`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
`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?