PharmacoSet: PharmacoSet constructor

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

PharmacoSet constructor

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(),
  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?
...	Catch and parse any renamed constructor arguments.

Value

An object of class PharmacoSet

Examples

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

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.