CoreSet: CoreSet constructor

In CoreGx: Classes and Functions to Serve as the Basis for Other 'Gx' Packages

Description

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. For a much more detailed instruction on creating CoreSets, please see the "CreatingCoreSet" vignette.

Usage

CoreSet(name, molecularProfiles = list(), cell = 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)),
  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 containg the annotations for all the cell lines 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, curationTissue	A data.frame mapping the names for cells and tissues used in the data set to universal identifiers used between different CoreSet objects
datasetType	A character string of 'sensitivity', 'preturbation', or both detailing what type of data can be found in the CoreSet, for proper processing of the data
verify	boolean Should the function verify the CoreSet and print out any errors it finds after construction?

Value

An object of class CoreSet

Examples

 
## For help creating a CoreSet object, please see the following vignette:
browseVignettes("PharmacoGx")

CoreGx documentation built on Dec. 20, 2019, 1:08 a.m.