PharmacoSet {PharmacoGx} | R Documentation

## 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(),
      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")

[Package PharmacoGx version 2.4.0 Index]