PharmacoSet: PharmacoSet constructor

In PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Description

A constructor that simplifies the process of creating PharmacoSets, 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 PharmacoSet methods. For a much more detailed instruction on creating PharmacoSets, please see the "CreatingPharmacoSet" vignette.

Usage

PharmacoSet(
  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 SummarizedExperiment objects containing molecular profiles for each molecular data type.
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 containg the annotations for all the drugs
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	A data.frame summarizing the available sensitivity/perturbation data
perturbationN	A data.frame summarizing the available sensitivity/perturbation data
curationDrug, curationCell, curationTissue	A data.frame mapping the names for drugs, cells and tissues used in the data set to universal identifiers used between different PharmacoSet 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 PharmacoSet

Examples

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

PharmacoGx documentation built on Feb. 28, 2021, 2 a.m.