ToxicoSet: 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 <U+2013> 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