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.

Return cell line metadata from a object

Generic for phenoInfo method

Generic for phenoInfo replace method

Generic for molecularProfiles method

Generic for molecularProfiles replace method

Generic for featureInfo method

Generic for featureInfo replace method

Get the senstivity information DataFrame from a object object

Set the sensitivityInfo DataFrame in a object object

Get the sensitivityProfiles data.frame from a object object

Set the sensitivityProfiles in a object object

Get the types of sensitivity measurements from a object object

A generic for the cellNames method

A generic for the cellNames replacement method

Return the feature names for the specified molecular data type

A generic for the dateCreated method

Retrun the name of the PharmacoSet object

A generic for the pertNumber method

A generic for the sensNumber method

A generic for the pertNumber method

A generic for the sensNumber method

Usage

## S4 method for signature 'PharmacoSet'
cellInfo(object)

## S4 method for signature 'PharmacoSet'
drugInfo(object)

## S4 replacement method for signature 'PharmacoSet,data.frame'
drugInfo(object) <- value

## S4 method for signature 'PharmacoSet'
phenoInfo(object, mDataType)

## S4 replacement method for signature 'PharmacoSet,character,DataFrame'
phenoInfo(object, mDataType) <- value

## S4 method for signature 'PharmacoSet'
molecularProfiles(object, mDataType, assay)

## S4 replacement method for signature 'PharmacoSet,character,character,matrix'
molecularProfiles(object, mDataType, assay) <- value

## S4 replacement method for signature 'PharmacoSet,character,missing,matrix'
molecularProfiles(object, mDataType, assay) <- value

## S4 method for signature 'PharmacoSet'
featureInfo(object, mDataType)

## S4 replacement method for signature 'PharmacoSet,character,DataFrame'
featureInfo(object, mDataType) <- value

## S4 method for signature 'PharmacoSet'
sensitivityInfo(object)

## S4 replacement method for signature 'PharmacoSet,data.frame'
sensitivityInfo(object) <- value

## S4 method for signature 'PharmacoSet'
sensitivityProfiles(object)

## S4 replacement method for signature 'PharmacoSet,data.frame'
sensitivityProfiles(object) <- value

## S4 replacement method for signature 'PharmacoSet,matrix'
sensitivityProfiles(object) <- value

## S4 method for signature 'PharmacoSet'
sensitivityMeasures(object)

## S4 method for signature 'PharmacoSet'
drugNames(object)

## S4 replacement method for signature 'PharmacoSet,character'
drugNames(object) <- value

## S4 method for signature 'PharmacoSet'
cellNames(object)

## S4 replacement method for signature 'PharmacoSet,character'
cellNames(object) <- value

## S4 method for signature 'PharmacoSet,character'
fNames(object, mDataType)

## S4 method for signature 'PharmacoSet'
dateCreated(object)

## S4 method for signature 'PharmacoSet'
name(object)

## S4 method for signature 'PharmacoSet'
pertNumber(object)

## S4 method for signature 'PharmacoSet'
sensNumber(object)

## S4 replacement method for signature 'PharmacoSet,array'
pertNumber(object) <- value

## S4 replacement method for signature 'PharmacoSet,matrix'
sensNumber(object) <- value

Arguments

object

A PharmacoSet

value

A new data.frame with the number of sensitivity experiments per drug and cell line

mDataType

The molecular data type to return feature names for

assay

character Name or index of the assay data to return

Value

An object of the PharmacoSet class

a data.frame with the cell annotations

a data.frame with the experiment info

The updated PharmacoSet

a matrix of data for the given mDataType and assay

Updated PharmacoSet

a data.frame with the experiment info

Updated PharmacoSet

a DataFrame with the experiment info

Updated PharmacoSet

a data.frame with the experiment info

Updated PharmacoSet

A character vector of all the available sensitivity measures

A vector of the cell names used in the PharmacoSet

Updated PharmacoSet

A character vector of the feature names

The date the PharmacoSet was created

The name of the PharmacoSet

A 3D array with the number of perturbation experiments per drug and cell line, and data type

A data.frame with the number of sensitivity experiments per drug and cell line

The updated PharmacoSet

The updated PharmacoSet

Methods (by generic)

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

Examples

data(CCLEsmall)
cellInf <- cellInfo(CCLEsmall)

data(CCLEsmall)
phenoInf <- phenoInfo(CCLEsmall, mDataType="rna")

data(CCLEsmall)
phenoInfo(CCLEsmall, mDataType="rna") <- phenoInfo(CCLEsmall, mDataType="rna")

data(CCLEsmall)
molProf <- molecularProfiles(CCLEsmall, "rna")

data(CCLEsmall)
molecularProfiles(CCLEsmall, "rna") <- molecularProfiles(CCLEsmall, "rna")

data(CCLEsmall)
featInf <- featureInfo(CCLEsmall, "rna")

data(CCLEsmall)
featureInfo(CCLEsmall, "rna") <- featureInfo(CCLEsmall, "rna")

data(CCLEsmall)
sensInf <- sensitivityInfo(CCLEsmall)

data(CCLEsmall)
sensitivityInfo(CCLEsmall) <- sensitivityInfo(CCLEsmall)

data(CCLEsmall)
sensProf <- sensitivityProfiles(CCLEsmall)

data(CCLEsmall)
sensitivityProfiles(CCLEsmall) <- sensitivityProfiles(CCLEsmall)

data(CCLEsmall)
sensMeas <- sensitivityMeasures(CCLEsmall)

data(CCLEsmall)
cellNames(CCLEsmall)

data(CCLEsmall)
cellNames(CCLEsmall) <- cellNames(CCLEsmall)

data(CCLEsmall)
fNames(CCLEsmall, "rna")

data(CCLEsmall)
dateCreated(CCLEsmall)

data(CCLEsmall)
name(CCLEsmall)

data(CCLEsmall)
pertNumber(CCLEsmall)

data(CCLEsmall)
sensNumber(CCLEsmall)

data(CCLEsmall)
pertNumber(CCLEsmall) <- pertNumber(CCLEsmall)

data(CCLEsmall)
sensNumber(CCLEsmall) <- sensNumber(CCLEsmall)


[Package PharmacoGx version 2.0.9 Index]