PharmacoSet-class: A Class to Contain PharmacoGenomic datasets together with...
In PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Description Usage Arguments Value Methods (by generic) Slots Examples

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

Get the names of all cell-lines available in a 'PharmacoSet' object

Update the names of cell lines available in a 'PharmacoSet' object

Get the data that a 'PharmacoSet' object was updated

A generic for the sensNumber method

Retrieve information from the

Get the names of all drugs available in a specified 'PharmacoSet' object

Set the drug names available in a PharmacoSet object

Return the feature names for the specified molecular data type

Get the molecular profile data for the specified molecular data type

Update the molecular profile data for the specified datatype in the specified pSet object

Returns the molecular data names for the 'PharmacoSet' object

Get the molecular profile data for the specified molecular data type

Update the molecular profile data for the specified datatype in the specified pSet object

Return the name of the PharmacoSet object

Return the name of the 'PharmacoSet' object

Get the perturbation number for a specified 'PharmcoSet' object

Set the perturbation number for a specified 'PharmacoSet' object

Get the phenotype information for a specified molecular datatype

Update the phenotype information for a specified molecular data type in a specified pSet object

Get the sensitivity numbers for a 'PharmacoSet' object

Get the senstivity information DataFrame from a PharmacoSet object

Set the sensitivityInfo DataFrame in a PharmacoSet object

Get the types of sensitivity measurements from a object object

Get the types of sensitivity measurements available in a PharmacoSet object

Get the sensitivityProfiles data.frame from a PharmacoSet object

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

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

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

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

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

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

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

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

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

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

## 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'
mDataNames(object)

## 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'
molecularProfilesSlot(object)

## S4 replacement method for signature 'PharmacoSet,list'
molecularProfilesSlot(object) <- value

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

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

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

## S4 replacement method for signature 'PharmacoSet,array'
pertNumber(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'
sensNumber(object)

## S4 method for signature 'PharmacoSet'
sensitivityInfo(object, dimension, ...)

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

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

## S4 replacement method for signature 'PharmacoSet,character'
sensitivityMeasures(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'
sensitivityRaw(object)

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

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

## S4 replacement method for signature 'PharmacoSet,list'
sensitivitySlot(object) <- value

`object`	A `PharmacoSet` to extract the raw sensitivity data from
`value`	A `list` of new sensitivity slot data for the pSet
`mDataType`	the type of molecular data
`assay`	['character'] Name or index of the assay data to return
`dimension`	['character'] Optional name of the dimension to extract, either 'cells' or 'drugs'. Only used if the sensitivity slot contains a 'LongTable' object instead of a 'list'.
`...`	Additional arguments to the rowData or colData 'LongTable' methods. Only used if the sensitivity slot contains a 'LongTable' object instead of a 'list'.

An object of the PharmacoSet class

a data.frame with the cell annotations

A vector of the cell names used in the PharmacoSet

Updated ['PharmacoSet']

['character'] The date the 'PharmacoSet' was created

The updated PharmacoSet

A ['data.frame'] containg annotatations for all drugs in the object

A ['PharmacoSet'] with updated drug annotations in the '@drug' slot

A ['character'] vector containg the names of drugs in the pSet

The updated ['PharmacoSet'] object

A ['character'] vector of the feature names

A ['data.frame'] with the feature annotations for the specified 'mDataType'

Updated PharmacoSet

Vector of names of the molecular data types

a ['matrix'] of data for the given mDataType and assay

Updated ['PharmacoSet']

A ['list'] of 'SummarizedExperiment' objects, named by molecular data type

['character'] The name of the 'PharmacoSet'

The name of the PharmacoSet

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

The updated ['PharmacoSet']

a ['data.frame'] with the phenotype information for the specified molecular data type

The updated PharmacoSet

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

a ['DataFrame'] with the experiment info

Updated PharmacoSet

A ['character'] vector of all the available sensitivity measures

a data.frame with the experiment info

['invisible'] Updates the 'PharmacoSet' object.

A array containing the raw sensitivity data

A copy of the PharmacoSet containing the updated sensitivty data

A list of the sensitivity slot contents

A copy of the PharmacoSet containing the updated sensitivty slot

cellInfo:
cellNames: Return the cell names used in the dataset
cellNames<-: Update the cell names used in the dataset
dateCreated: Return the date the PharmacoSet was created
sensNumber<-: Update the summary of available sensitivity experiments
drugInfo: Returns the annotations for all the drugs tested in the PharmacoSet
drugInfo<-: Update the drug annotations
drugNames: Return the names of the drugs used in the PharmacoSet
drugNames<-: Update the drug names used in the dataset
fNames: Return the feature names used in the dataset
featureInfo: Return the feature info for the given molecular datatype
featureInfo<-: Replace the gene info for the molecular data
mDataNames: Returns the names of molecular data types in a PharmacoSet
molecularProfiles: Return the given type of molecular data from the PharmacoSet
molecularProfiles<-: Update the given type of molecular data from the PharmacoSet
molecularProfiles<-: Update the given type of molecular data from the PharmacoSet
molecularProfilesSlot: Getter for the molecular profiles slot
molecularProfilesSlot<-: Setter for the molecular profiles slot
name: Return the name of the PharmacoSet
name<-: Return the name of the PharmacoSet
pertNumber: Return the summary of available perturbation experiments
pertNumber<-: Update the summary of available perturbation experiments
phenoInfo: Return the experiment info from the given type of molecular data in PharmacoSet
phenoInfo<-: Update the given type of molecular data experiment info in the PharmacoSet
sensNumber: Return the summary of available sensitivity experiments
sensitivityInfo: Return the drug dose sensitivity experiment info
sensitivityInfo<-: Update the metadata for the treatment response experiments in the sensitivity slot.
sensitivityMeasures: returns the available sensitivity profile summaries, for example, whether there are IC50 values available
sensitivityMeasures<-: returns the available sensitivity profile summaries, for example, whether there are IC50 values available
sensitivityProfiles: Return the sensitivity profile summary values for the treatment response experiment data in the sensitivity slot.
sensitivityProfiles<-: Update the sensitivity profiles for a 'PharmacoSet' object.
sensitivityProfiles<-: Update the sensitivity profiles for a 'PharmacoSet' object.
sensitivityRaw: Retrive the raw dose and viability data from a pSet
sensitivityRaw<-: Update the raw dose and viability data in a pSet object
sensitivitySlot: Retrieve the contents of the sensitivity slot
sensitivitySlot<-: Set the raw dose and viability data for an pSet and return and updated copty

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

data(CCLEsmall)
cellInf <- cellInfo(CCLEsmall)

data(CCLEsmall)
cellNames(CCLEsmall)

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

data(CCLEsmall)
dateCreated(CCLEsmall)

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

data(CCLEsmall)
drugInf <- drugInfo(CCLEsmall)

data(CCLEsmall)
drugInf <- drugInfo(CCLEsmall)

data(CCLEsmall)
drugNames(CCLEsmall)

data(CCLEsmall)
drugNames(CCLEsmall) <- drugNames(CCLEsmall)

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

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

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

data(CCLEsmall)
mDataNames(CCLEsmall)

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

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

data(CCLEsmall)
molProfSlot <- molecularProfilesSlot(CCLEsmall)

data(CCLEsmall)
molecularProfilesSlot(CCLEsmall) <- molecularProfilesSlot(CCLEsmall)

data(CCLEsmall)
name(CCLEsmall)

data(CCLEsmall)
name(CCLEsmall) <- 'CCLEsmall'

data(CCLEsmall)
pertNumber(CCLEsmall)

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

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

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

data(CCLEsmall)
sensNumber(CCLEsmall)

data(CCLEsmall)
sensInf <- sensitivityInfo(CCLEsmall)

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

data(CCLEsmall)
sensMeas <- sensitivityMeasures(CCLEsmall)

data(CCLEsmall)
sensMeas <- sensitivityMeasures(CCLEsmall)

data(CCLEsmall)
sensProf <- sensitivityProfiles(CCLEsmall)

data(GDSCsmall)
sensitivityProfiles(GDSCsmall) <- sensitivityProfiles(GDSCsmall)

data(GDSCsmall)
sensitivityProfiles(GDSCsmall) <- sensitivityProfiles(GDSCsmall)

data(CCLEsmall)
sensitivityRaw(CCLEsmall)

data(CCLEsmall)
sensitivityRaw(CCLEsmall) <- sensitivityRaw(CCLEsmall)

data(CCLEsmall)
sensitivitySlot(CCLEsmall)

data(CCLEsmall)
sensitivitySlot(CCLEsmall) <- sensitivitySlot(CCLEsmall)