PharmacoSet-class {PharmacoGx} | R Documentation

## A Class to Contain PharmacoGenomic datasets together with their curations

### Description

The PharmacoSet (pSet) class was developed to contain and organise large PharmacoGenomic datasets, and aid in their metanalysis. It was designed primarily to allow bioinformaticians and biologists to work with data at the level of genes, drugs and cell lines, providing a more naturally intuitive interface and simplifying analyses between several datasets. As such, it was designed to be flexible enough to hold datasets of two different natures while providing a common interface. The class can accomidate datasets containing both drug dose response data, as well as datasets contaning genetic profiles of cell lines pre and post treatement with compounds, known respecitively as sensitivity and perturbation datasets.

### Arguments

`object` | A `PharmacoSet` object
`mDataType` | A `character` with the type of molecular data to return/update
`value` | A replacement value

### Value

An object of the PharmacoSet class

### Slots

`annotation`

  A `list` of annotation data about the PharmacoSet, including the `$name` and the session information for how the object was creating, detailing the exact versions of R and all the packages used

`molecularProfiles`

  A `list` containing `SummarizedExperiment` type object for holding data for RNA, DNA, SNP and CNV measurements, with associated `fData` and `pData` containing the row and column metadata

`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 profiled in the data set, across all data types

`sensitivity`

  A `list` containing all the data for the sensitivity experiments, including `$info`, a `data.frame` containing the experimental info,`$raw` a 3D `array` containing raw data, `$profiles`, a `data.frame` containing sensitivity profiles statistics, and `$n`, a `data.frame` detailing the number of experiments for each cell-drug pair

`perturbation`

  A `list` containting `$n`, a `data.frame` summarizing the available perturbation data,

`curation`

  A `list` containing mappings for `$drug`, `cell`, `tissue` names used in the data set to universal identifiers used between different PharmacoSet objects

`datasetType`

  A `character` string of 'sensitivity', 'perturbation', or both detailing what type of data can be found in the PharmacoSet, for proper processing of the data

[Package PharmacoGx version 2.4.0 Index]