ToxicoSet-class {ToxicoGx} | R Documentation

## Class to contain Toxico-genomic Data

### Description

The ToxicoSet (tSet) class was development to contain and organise large ToxicGenomic datasets as well as provide useful tools for interacting with this data. Functions are included for exploring the relationship between survival fraction and gene expression in cultured human and rat tissues during exposure to a wide ranges of compounds. Features include plotting dose and exposure time curves, calculating AUC, fitting linear models and computing sensitivity signatures.

Get the cell line annotations in a ToxicoSet

Set cell line annotations for a ToxicoSet object

Get names of cell lines in a ToxicoSet object

Set the cell line names in a TocicoSet object

Get the date a ToxicoSet object was created

Get the feature names in a ToxicoSet object for the specified molecular data type

Set the feature names in a ToxicoSet object for the specified molecular data type

Set the feature annotations for a specficied molecular data type

Get the molecular profile data associated with the specific molecular data

Set the molecular profile data assciated with the specificied molecular data type

Get an array of the number of pertubration experiments per drug and cell line in a ToxicoSet object

Set the number of perturbation experiments per drug and cell line and molecular data type in a ToxicoSet object

Get the phenotype annotations for cell lines with the specificed molecular data type

Set the phenotype annotations for cell lines with the selected molecular data type.

Get the number of sensitivity experiments per drug and cell line in a ToxicoSet

Set the number of sensitivity experiments per drug and cell line in a ToxicoSet object

Get the annotations for the sensitivity experiments in the ToxicoSet

Set the annotations for sensitivity experiments in this ToxicSet

Get the avilable measurments for sensitivity experiments in a ToxicoSet

Get the data for sensitivty experiments on cell lines in a ToxicoSet

Set the data for sensitivity experiments on cell lines in a ToxicoSet

### Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

### Arguments

`object` | A `ToxicoSet` to extract the raw sensitivity data from
`value` | A `list` of new sensitivity slot data for the tSet
`mDataType` | A `character` with the type of molecular data to return/update
`assay` | `character` Name or index of the assay data to return
`...` | Allow new parameters to be defined for this generic

### Value

An object of the ToxicoSet class

a `data.frame` with the cell annotations

Updated `ToxicoSet`

A vector of the cell names used in the ToxicoSet

Updated `ToxicoSet`

The date the ToxicoSet was created

A `character` vector of the feature names

Updated `ToxicoSet`

Updated `ToxicoSet`

Updated `ToxicoSet`

A `list` containing the molecularProfiles from a tSet

A copy of the `ToxicoSet` with the molecularProfiles slot updated

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

The updated `ToxicoSet`

a `Dframe` with the experiment info

The updated `ToxicoSet`

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

The updated `ToxicoSet`

a `data.frame` with the experiment info

Updated `ToxicoSet`

A `character` vector of all the available sensitivity measures

a `data.frame` with the experiment info

Updated `ToxicoSet`

### Methods (by generic)

- `annotation`: Retrieve the annotations slot form an tSet

- `annotation<-`: Update the annotation slot of a tSet

- `cellInfo`: Returns the annotations for all the cell lines tested on in the ToxicoSet

- `cellInfo<-`: Returns the annotations for all the cell lines tested on in the ToxicoSet

- `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 tSet

- `curation<-`: Update the annotation slot of a tSet

- `datasetType<-`: Update the dataset type of an tSet and return a copy of the updated object

- `dateCreated`: Return the date the ToxicoSet was created

- `datasetType`: Update the dataset type of an tSet and return a copy of the updated object

- `drugInfo`: Returns the annotations for all the drugs tested in the ToxicoSet

- `drugInfo<-`: Update the drug annotations

- `drugNames`: Return the names of the drugs used in the ToxicoSet

- `drugNames<-`: Update the drug names used in the dataset

- `fNames`: Return the feature names used in the dataset

- `fNames<-`: Update the feature names used in the dataset

- `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 ToxicoSet

- `molecularProfiles<-`: Update the given type of molecular data from the ToxicoSet

- `molecularProfiles<-`: Update the given type of molecular data from the ToxicoSet

- `molecularProfilesSlot`: Get contents of molecularProfiles slot

- `molecularProfilesSlot<-`: Update the molecular profiles slot of a ToxicoSet and returns the updated copy

- `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 ToxicoSet

- `phenoInfo<-`: Update the the given type of molecular data experiment info in the ToxicoSet

- `sensNumber`: Return the summary of available sensitivity experiments

- `sensNumber<-`: Update the summary of available sensitivity experiments

- `sensitivityInfo`: Return the drug 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 drug dose sensitivity

- `sensitivityProfiles<-`: Update the phenotypic data for the drug dose sensitivity

- `sensitivityProfiles<-`: Update the phenotypic data for the drug dose sensitivity

- `sensitivityRaw`: Retrive the raw dose and viability data from an tSet

- `sensitivityRaw<-`: Set the raw dose and viability data for a tSet and return and updated copty

- `sensitivitySlot`: Retrieves the contents of the sensitivity slot

- `sensitivitySlot<-`: Set the raw dose and viability data for an tSet and return and updated copy

### Slots

`annotation`

  A `list` of annotation data about the ToxicoSet, 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 ToxicoSet objects

`datasetType`

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

### Examples

    data(TGGATESsmall)
    cellInfo <- cellInfo(TGGATESsmall)

    data(TGGATESsmall)
    cellInfo(TGGATESsmall) <- cellInfo(TGGATESsmall)

    cellNames(TGGATESsmall)

    data(TGGATESsmall)
    cellNames(TGGATESsmall) <- cellNames(TGGATESsmall)

    dateCreated(TGGATESsmall)

    data(TGGATESsmall)
    datasetType(TGGATESsmall)

    fNames(TGGATESsmall, "rna")[seq_len(10)]

    data(TGGATESsmall)
    cellNames(TGGATESsmall) <- cellNames(TGGATESsmall)

    data(TGGATESsmall)
    featureInfo <- featureInfo(TGGATESsmall, "rna")[seq_len(10),]

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

    data(TGGATESsmall)
    TGGATES_mProf <- molecularProfiles(TGGATESsmall, "rna")[seq_len(10),]

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

    data(TGGATESsmall)
    molecularProfilesSlot(TGGATESsmall)

    data(TGGATESsmall)
    molecularProfilesSlot(TGGATESsmall) <- molecularProfilesSlot(TGGATESsmall)

    pertNumber(TGGATESsmall)

    pertNumber(TGGATESsmall) <- pertNumber(TGGATESsmall)

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

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

    sensNumber(TGGATESsmall)

    sensNumber(TGGATESsmall) <- sensNumber(TGGATESsmall)

    data(TGGATESsmall)
    sensInf<- sensitivityInfo(TGGATESsmall)[seq_len(10),]

    data(TGGATESsmall)
    sensitivityInfo(TGGATESsmall) <- sensitivityInfo(TGGATESsmall)

    sensitivityMeasures(TGGATESsmall)

    data(TGGATESsmall)
    sensProf <- sensitivityProfiles(TGGATESsmall)

    sensitivityProfiles(TGGATESsmall) <- sensitivityProfiles(TGGATESsmall)

    data(TGGATESsmall)
    sensitivitySlot(TGGATESsmall)

    data(TGGATESsmall)
    sensitivitySlot(TGGATESsmall) <- sensitivitySlot(TGGATESsmall)

[Package ToxicoGx version 1.4.0 Index]