ToxicoSet {ToxicoGx} | 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(),
      cell = data.frame(),
      drug = 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)),
      curationDrug = data.frame(),
      curationCell = 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 ExpressionSet objects containing molecular profiles
`cell` | A `data.frame` containing the annotations for all the cell lines profiled in the data set, across all data types
`drug` | A `data.frame` containing the annotations for all the drugs profiled in the data set, across all data types
`sensitivityInfo` | A `data.frame` containing the information for the sensitivity experiments
`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
`curationCell, curationDrug, curationTissue` | A `data.frame` mapping the names for cells, drugs, and tissues used in the data set to universal identifiers used between different ToxicoSet objects
`datasetType` | A `character` string of "sensitivity", "perturbation", or both detailing what type of data can be found in the ToxicoSet, for proper processing of the data
`verify` | `boolean` Should the function verify the ToxicoSet and print out any errors it finds after construction?

### Value

An object of class `ToxicoSet`

[Package ToxicoGx version 1.4.0 Index]