RadioSet-class: A Class to Contain RadioGenomic datasets together with their...
In RadioGx: Analysis of Large-Scale Radio-Genomic Data

Description Usage Arguments Value Methods (by generic) Slots Examples

The RadioSet (RSet) class was developed to contain and organise large RadioGenomic datasets, and aid in their metanalysis. It was designed primarily to allow bioinformaticians and biologists to work with data at the level of genes 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 radiation 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.

Get cell line information from a RadioSet object

Set cell line annotations for a RadioSet object

Get the names of all cell lines in a RadioSet object

Set the names of all cell lines in a RadioSet object

A generic for retrieving the dataset type of an rSet object

A generic for updating the dataset type of a RadioSet object

Get the date a RadioSet object was created

Return the feature names for the specified molecular data type

Setter for the feature names of a SummarizedExperiment in the molecularProfiles slot

Getter method for the feature data of the given molecular data type

Setter method for the feature data of the given molecular data type

Getter method for the molecular profile data of the given molecular data type

Setter method for the molecular profile data of the given molecular data type

Get the name of a RadioSet

Get a summary of available perturbation experiments

Get the summary of the available sensitivity experiments in the RadioSet

Getter method for the phenotype information of a given molecular data type

Setter method for the phenotype information of a given molecular data type

Get a summary of the available sensitivity experiments in the RadioSet

Set the summary of the available sensitivity experiments in the RadioSet

Get the sensitivity information for the cell lines in the RadioSet

Set the sensitivity information for the cell lines in the RadioSet

Get the types of sensitivity measurements available in a RadioSet

Get the sensitivity values for the cell lines in the RadioSet

Set the sensitivity information for the cell lines in the RadioSet

## S4 method for signature 'RadioSet'
annotation(object)

## S4 replacement method for signature 'RadioSet,list'
annotation(object) <- value

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

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

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

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

## S4 method for signature 'RadioSet'
curation(object)

## S4 replacement method for signature 'RadioSet,list'
curation(object) <- value

## S4 method for signature 'RadioSet'
datasetType(object)

## S4 replacement method for signature 'RadioSet'
datasetType(object) <- value

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

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

## S4 replacement method for signature 'RadioSet,character,character'
fNames(object, mDataType) <- value

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

## S4 replacement method for signature 'RadioSet,character,data.frame'
featureInfo(object, mDataType) <- value

## S4 method for signature 'RadioSet,character'
molecularProfiles(object, mDataType)

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

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

## S4 method for signature 'RadioSet'
molecularProfilesSlot(object)

## S4 replacement method for signature 'RadioSet,ANY'
molecularProfilesSlot(object) <- value

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

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

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

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

## S4 replacement method for signature 'RadioSet,character,data.frame'
phenoInfo(object, mDataType) <- value

## S4 method for signature 'RadioSet'
radiationInfo(object)

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

## S4 method for signature 'RadioSet'
radiationTypes(object)

## S4 replacement method for signature 'RadioSet,character'
radiationTypes(object) <- value

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

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

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

## S4 replacement method for signature 'RadioSet,DataFrame'
sensitivityInfo(object) <- value

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

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

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

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

## S4 method for signature 'RadioSet'
sensitivityRaw(object)

## S4 replacement method for signature 'RadioSet,ANY'
sensitivityRaw(object) <- value

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

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

`object`	A `RadioSet` to extract the raw sensitivity data from
`value`	A `list` of new sensitivity slot data for the rSet
`mDataType`	the type of molecular data
`assay`	`character` Name or index of the assay data to return

An object of the RadioSet class

A list of named annotaiton

A copy of the RadioSet with the updated annotation slot

a data.frame with the cell annotations

Updated RadioSet

A vector of the cell line names in the RadioSet

Updated RadioSet

A list of unique cell and tissue identifiers to check validity of an rSet

A copy of the RadioSet with the updated curation slot

A character vector containing the dataset tpye

The date the RadioSet was created

A character vector of the feature names

Updated RadioSet

A DataFrame containing the feature information

Updated RadioSet

a data.frame with the experiment info

Updated RadioSet

A list containing the molecularProfiles from a cSet

A copy of the RadioSet with the molecularProfiles slot updated

The name of the RadioSet

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

The updated RadioSet

a data.frame with the experiment info

The updated RadioSet

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

The updated RadioSet

a DataFrame with the experiment info

Updated RadioSet

A character vector of all the available sensitivity measures

a data.frame with the experiment info

Updated RadioSet

A array containing the raw sensitivity data

A copy of the RadioSet containing the updated sensitivty data

A list of the sensitivity slot contents

A copy of the RadioSet containing the updated sensitivty slot

annotation: Retrieve the annotations slot form an rSet
annotation<-: Update the annotation slot of a tSet
cellInfo: Returns the annotations for all the cell lines tested on in the RadioSet
cellInfo<-: Update the cell line annotations
cellNames: Return the cell names used in the dataset
cellNames<-: Update the cell names used in the dataset
curation: Retrieve the curation slot form an rSet
curation<-: Update the curations for cell and tissue types in an rSet object
datasetType: Return the dataset type of an rSet object
datasetType<-: Update the dataset type of an rSet and return a copy of the updated object
dateCreated: Return the date the RadioSet was created
fNames: Return the feature names used in the dataset
fNames<-: Set the feature names for a given molecular data type
featureInfo: Return the feature info for the given molecular data
featureInfo<-: Replace the gene info for the molecular data
molecularProfiles: Return the given type of molecular data from the RadioSet
molecularProfiles<-: Update the given type of molecular data from the RadioSet
molecularProfiles<-: Update the given type of molecular data from the RadioSet
molecularProfilesSlot: Get contents of molecularProfiles slot
molecularProfilesSlot<-: Update the molecular profiles slot of a RadioSet and returns the updated copy
name: Return the name of the RadioSet
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 RadioSet
phenoInfo<-: Update the the given type of molecular data experiment info in the RadioSet
radiationInfo: Returns the annotations for all the radiations tested in the RadioSet
radiationInfo<-: Update the radiation annotations
radiationTypes: Return the names of the radiations used in the RadioSet
radiationTypes<-: Update the radiation names used in the dataset
sensNumber: Return a summary of available sensitivity experiments
sensNumber<-: Update the summary of available sensitivity experiments
sensitivityInfo: Return the radiation dose sensitivity experiment info
sensitivityInfo<-: Update the sensitivity experiment info
sensitivityMeasures: Returns the available sensitivity profile summaries, for example, whether there are IC50 values available
sensitivityProfiles: Return the phenotypic data for the radiation dose sensitivity
sensitivityProfiles<-: Update the phenotypic data for the radiation dose sensitivity
sensitivityProfiles<-: Update the phenotypic data for the radiation dose sensitivity
sensitivityRaw: Retrive the raw dose and viability data from an rSet
sensitivityRaw<-: Update the raw dose and viability data in an rSet object
sensitivitySlot: Retrieve the contents of the sensitivity slot
sensitivitySlot<-: Set the raw dose and viability data for an rSet and return and updated copty

annotation: A list of annotation data about the RadioSet, 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 4 SummarizedExperiment type object for holding data for RNA, DNA, SNP and Copy Number Variation measurements respectively, with associated fData and pData containing the row and column metadata
cell: A data.frame containg the annotations for all the cell lines profiled in the data set, across all data types
radiation: A data.frame containg the annotations for all the radiation treatment types used in the in the dataset, 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-radiation type pair
perturbation: A list containting $n, a data.frame summarizing the available perturbation data,
curation: A list containing mappings for cell and tissue names used in the data set to universal identifiers used between different RadioSet objects
datasetType: A character string of 'sensitivity', 'perturbation', or both detailing what type of data can be found in the RadioSet, for proper processing of the data

data(clevelandSmall)
annotation(clevelandSmall)

data(clevelandSmall)
annotation(clevelandSmall) <- annotation(clevelandSmall)

data(clevelandSmall)
cellInf <- cellInfo(clevelandSmall)

data(clevelandSmall)
cellInfo(clevelandSmall) <- cellInfo(clevelandSmall)

data(clevelandSmall)
cellNames(clevelandSmall)

data(clevelandSmall)
cellNames(clevelandSmall) <- cellNames(clevelandSmall)

data(clevelandSmall)
curation(clevelandSmall)

data(clevelandSmall)
curation(clevelandSmall) <- curation(clevelandSmall)

data(clevelandSmall)
datasetType(clevelandSmall)

data(clevelandSmall)
datasetType(clevelandSmall)

dateCreated(clevelandSmall)

data(clevelandSmall)
fNames(clevelandSmall, "rna")

data(clevelandSmall)
fNames(clevelandSmall, 'rna') <- fNames(clevelandSmall, 'rna')

featInf <- featureInfo(clevelandSmall, "rna")

featureInfo(clevelandSmall, "rna") <- featureInfo(clevelandSmall, "rna")

data(clevelandSmall)
Cleveland_mProf <- molecularProfiles(clevelandSmall, "rna")

molecularProfiles(clevelandSmall, "rna") <-
  molecularProfiles(clevelandSmall, "rna")

data(clevelandSmall)
molecularProfilesSlot(clevelandSmall)

data(clevelandSmall_cSet)
molecularProfilesSlot(clevelandSmall_cSet) <- molecularProfilesSlot(clevelandSmall_cSet)

name(clevelandSmall)

data(clevelandSmall)
pertNumber(clevelandSmall)

pertNumber(clevelandSmall) <- pertNumber(clevelandSmall)

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

phenoInfo(clevelandSmall, mDataType="rna") <- phenoInfo(clevelandSmall,
  mDataType="rna")

data(clevelandSmall)
sensNumber(clevelandSmall)

sensNumber(clevelandSmall) <- sensNumber(clevelandSmall)

sensInf<- sensitivityInfo(clevelandSmall)

sensitivityInfo(clevelandSmall) <- sensitivityInfo(clevelandSmall)

data(clevelandSmall)
sensMeas <- sensitivityMeasures(clevelandSmall)

sensProf <- sensitivityProfiles(clevelandSmall)

sensitivityProfiles(clevelandSmall) <- sensitivityProfiles(clevelandSmall)

data(clevelandSmall)
sensitivityRaw(clevelandSmall)

data(clevelandSmall)
sensitivityRaw(clevelandSmall) <- sensitivityRaw(clevelandSmall)

data(clevelandSmall)
sensitivitySlot(clevelandSmall)

data(clevelandSmall)
sensitivitySlot(clevelandSmall) <- sensitivitySlot(clevelandSmall)