RadioSet-class {RadioGx} | R Documentation

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

### Description

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

### Usage

    ## 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,ANY'
    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

### Arguments

`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

### Value

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

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

### Methods (by generic)

- `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

### Slots

`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

### Examples

    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)

[Package RadioGx version 1.4.0 Index]