PharmacoSet-accessors {PharmacoGx} | R Documentation

## Accessing and modifying information in a `PharmacoSet`

### Description

Documentation for the various setters and getters which allow manipulation of data in the slots of a `PharmacoSet` object.

### Usage

    ## 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'
    annotation(object)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    ## S4 replacement method for signature 'PharmacoSet'
    mDataNames(object) <- value

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

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

    ## 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 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_or_LongTable'
    sensitivitySlot(object) <- value

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

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

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

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

### Arguments

`object` | A `PharmacoSet` object.
`value` | See details.
`mDataType` | `character(1)` The name of a molecular datatype to access from the `molecularProfiles` of a `PharmacoSet` object.
`assay` | `character(1)` A valid assay name in the `SummarizedExperiment` of `@molecularProfiles` of a PharmacoSet object for data type `mDataType`.
`dimension` | See details.
`...` | See details.

### Details

#### drug slot accessors

drugInfo: `data.frame` Retrieve the drug metadata from a `PharmacoSet` objects `@drug` slot.

drugInfo: Update the `@drug` slot of a `PharmacoSet` object.

- value: `data.frame` of updated drug metadata to assign to a `PharmacoSet` objects `@drug` slot.

drugNames: `character()` The names of all drugs available in a specified `PharmacoSet` object.

drugNames<-: Set the drug names available in a PharmacoSet object.

- value: A `character` vector of the new drug names. Must have the same length equal to `nrow(drugInfo(object))`.

#### @annotation

annotation: A `list` of PharmacoSet annotations with items: 'name', the name of the object; 'dateCreated', date the object was created; 'sessionInfo', the `sessionInfo()` when the object was created; 'call', the R constructor call; and 'version', the object version.

annotation<-: Setter method for the annotation slot. Arguments:

- value: a `list` of annotations to update the PharmacoSet with.

#### @dateCreated

dateCreated: `character(1)` The date the `PharmacoSet` object was created, as returned by the `date()` function.

dateCreated<-: Update the 'dateCreated' item in the `annotation` slot of a `PharmacoSet` object. Arguments:

- value: A `character(1)` vector, as returned by the `date()` function.

name: `character(1)` The name of the `PharmacoSet`, retreived from the `@annotation` slot.

name<-: Update the `@annotation$name` value in a `PharmacoSet` object.

- value: `character(1)` The name of the `PharmacoSet` object.

cellInfo: `data.frame` Metadata for all cell-lines in a `PharmacoSet` object.

cellInfo<-: assign updated cell-line annotations to the `PharmacoSet` object. Arguments:

- value: a `data.frame` object.

cellNames: `character` Retrieve the rownames of the `data.frame` in the `cell` slot from a PharmacoSet object.

cellNames<-: assign new rownames to the cellInfo slot `data.frame` for a PharmacoSet object. Arguments:

- value: `character` vector of rownames for the `cellInfo(object)` `data.frame`.

#### @curation

curation: A `list` of curated mappings between identifiers in the PharmacoSet object and the original data publication. Contains three `data.frame`s, 'cell' with cell-line ids and 'tissue' with tissue ids and 'drug' with drug ids.

curation<-: Update the `curation` slot of a PharmacoSet object. Arugments:

- value: A `list` of `data.frame`s, one for each type of curated identifier. For a `PharmacoSet` object the slot should contain tissue, cell-line and drug id `data.frame`s.

#### datasetType slot

datasetType: `character(1)` The type treatment response in the `sensitivity` slot. Valid values are 'sensitivity', 'perturbation' or 'both'.

datasetType<-: Update the datasetType slot of a PharmacoSet object. Arguments:

- value: A `character(1)` vector with one of 'sensitivity', 'perturbation' or 'both'

#### @molecularProfiles

molecularProfiles: `matrix()` Retrieve an assay in a `SummarizedExperiment` from the `molecularProfiles` slot of a `PharmacoSet` object with the specified `mDataType`. Valid `mDataType` arguments can be found with `mDataNames(object)`. Arguments:

- assay: Optional `character(1)` vector specifying an assay in the `SummarizedExperiment` of the `molecularProfiles` slot of the `PharmacoSet` object for the specified `mDataType`. If excluded, defaults to modifying the first assay in the `SummarizedExperiment` for the given `mDataType`.

molecularProfiles<-: Update an assay in a `SummarizedExperiment` from the `molecularProfiles` slot of a PharmacoSet object with the specified `mDataType`. Valid `mDataType` arguments can be found with `mDataNames(object)`.

- assay: Optional `character(1)` vector specifying an assay in the `SummarizedExperiment` of the `molecularProfiles` slot of the `PharmacoSet` object for the specified `mDataType`. If excluded, defaults to modifying the first assay in the `SummarizedExperiment` for the given `mDataType`.

- value: A `matrix` of values to assign to the `assay` slot of the `SummarizedExperiment` for the selected `mDataType`. The rownames and column names must match the associated `SummarizedExperiment`.

featureInfo: Retrieve a `DataFrame` of feature metadata for the specified `mDataType` from the `molecularProfiles` slot of a `PharmacoSet` object. More specifically, retrieve the `@rowData` slot from the `SummarizedExperiment` from the `@molecularProfiles` of a `PharmacoSet` object with the name `mDataType`.

featureInfo<-: Update the `featureInfo(object, mDataType)` `DataFrame` with new feature metadata. Arguments:

- value: A `data.frame` or `DataFrame` with updated feature metadata for the specified molecular profile in the `molecularProfiles` slot of a `PharmacoSet` object.

phenoInfo: Return the `@colData` slot from the `SummarizedExperiment` of `mDataType`, containing sample-level metadata, from a `PharmacoSet` object.

phenoInfo<-: Update the `@colData` slot of the `SummarizedExperiment` of `mDataType` in the `@molecularProfiles` slot of a `PharmacoSet` object. This updates the sample-level metadata in-place.

- value: A `data.frame` or `DataFrame` object where rows are samples and columns are sample metadata.

fNames: `character()` The features names from the `rowData` slot of a `SummarizedExperiment` of `mDataType` within a `PharmacoSet` object.

fNames: Updates the rownames of the feature metadata (i.e., `rowData`) for a `SummarizedExperiment` of `mDataType` within a `PharmacoSet` object.

- value: `character()` A character vector of new features names for the `rowData` of the `SummarizedExperiment` of `mDataType` in the `@molecularProfiles` slot of a `PharmacoSet` object. Must be the same length as `nrow(featureInfo(object, mDataType))`, the number of rows in the feature metadata.

mDataNames: `character` Retrieve the names of the molecular data types available in the `molecularProfiles` slot of a `PharmacoSet` object. These are the options which can be used in the `mDataType` parameter of various `molecularProfiles` slot accessors methods.

mDataNames: Update the molecular data type names of the `molecularProfiles` slot of a PharmacoSet object. Arguments:

- value: `character` vector of molecular datatype names, with length equal to `length(molecularProfilesSlot(object))`.

molecularProfilesSlot: Return the contents of the `@molecularProfiles` slot of a `PharmacoSet` object. This will either be a `list` or `MultiAssayExperiment` of `SummarizedExperiment`s.

molecularProfilesSlot<-: Update the contents of the `@molecularProfiles` slot of a `PharmacoSet` object. Arguemnts:

- value: A `list` or `MultiAssayExperiment` of `SummarizedExperiment`s. The `list` and `assays` should be named for the molecular datatype in each `SummarizedExperiment`.

#### @sensitivity

##### Arguments:

- `dimension`: Optional `character(1)` One of 'drug', 'cell' or 'assay' to retrieve `rowData`, `colData` or the 'assay_metadata' assay from the `PharmacoSet` `@sensitvity` `LongTable` object, respectively. Ignored with warning if `@sensitivity` is not a `LongTable` object.

- `...`: Additional arguments to the `rowData` or `colData`. `LongTable` methods. Only used if the sensitivity slot contains a `LongTable` object instead of a `list` and the `dimension` argument is specified.

##### Methods:

sensitivityInfo: `DataFrame` or `data.frame` of sensitivity drug combo by cell-line metadata for the `PharmacoSet` object. When the `dimension` parameter is used, it allows retrieval of the dimension specific metadata from the `LongTable` object in `@sensitivity` of a PharmacoSet object.

sensitivityInfo<-: Update the `@sensitivity` slot metadata for a `PharmacoSet` object. When used without the `dimension` argument is behaves similar to the old PharmacoSet implementation, where the `@sensitivity` slot contained a list with a `$info` `data.frame` item. When the `dimension` arugment is used, more complicated assignments can occur where 'cell' modifies the `@sensitvity` `LongTable` colData, 'drug' the rowData and 'assay' the 'assay_metadata' assay. Arguments:

- value: A `data.frame` of treatment response experiment metadata, documenting experiment level metadata (mapping to drugs and cells). If the `@sensitivity` slot doesn't contain a `LongTable` and `dimension` is not specified, you can only modify existing columns as returned by `sensitivityInfo(object)`.

sensitivityMeaures: Get the 'sensitivityMeasures' available in a `PharmacoSet` object. Each measure reprents some summary of cell-line sensitivity to a given dryuh, such as ic50, ec50, AUC, AAC, etc. The results are returned as a `character` vector with all available metrics for the PSet object.

sensitivityMeaures: Update the sensitivity meaure in a `PharmacoSet` object. Thesee values are the column names of the 'profiles' assay and represent various compued sensitviity metrics such as ic50, ec50, AUC, AAC, etc.

- value: A `character` vector of new sensitivity measure names, the then length of the character vector must matcht he number of columns of the 'profiles' assay, excluding metadata and key columns.

sensitivityProfiles: Return the sensitivity profile summaries from the sensitivity slot. This data.frame cotanins vaarious sensitivity summary metrics, such as ic50, amax, EC50, aac, HS, etc as columns, with rows as drug by sample experiments.

sensitivityProfiles<-: Update the sensitivity profile summaries the sensitivity slot. Arguments: -value: A `data.frame` the the same number of rows as as returned by `sensitivityProfiles(object)`, but potentially modified columns, such as the computation of additional summary metrics.

sensitivityRaw: Access the raw sensitiity measurents for a PharmacoSet object. A 3D `array` where rows are experiment_ids, columns are doses and the third dimension is metric, either 'Dose' for the doses used or 'Viability' for the cell-line viability at that dose.

sensitvityRaw<-: Update the raw dose and viability data in a PharmacoSet.

- value: A 3D `array` object where rows are experiment_ids, columns are replicates and pages are c('Dose', 'Viability'), with the corresponding dose or viability measurement for that experiment_id and replicate.

sensNumber: Return a count of viability observations in a `PharmacoSet` object for each drug-combo by cell-line combination.

sensNumber<-: Update the 'n' item, which holds a matrix with a count of drug by cell-line experiment counts, in the `list` in `@sensitivity` slot of a `PharmacoSet` object. Will error when `@sensitviity` contains a `LongTable` object, since the counts are computed on the fly. Arguments:

- value: A `matrix` where rows are cells and columns are drugs, with a count of the number of experiments for each combination as the values.

pertNumber: `array` Summary of available perturbation experiments from in a `PharmacoSet` object. Returns a 3D `array` with the number of perturbation experiments per drug and cell line, and data type.

pertNumber<-: Update the `@perturbation$n` value in a `PharmacoSet` object, which stores a summary of the available perturbation experiments. Arguments:

- value: A new 3D `array` with the number of perturbation experiments per drug and cell line, and data type

### Value

Accessors: See details.

Setters: An updated `PharmacoSet` object, returned invisibly.

### Examples

    data(CCLEsmall)

    ## drug slot

    drugInfo(CCLEsmall)

    drugInfo(CCLEsmall) <- drugInfo(CCLEsmall)

    drugNames(CCLEsmall)

    drugNames(CCLEsmall) <- drugNames(CCLEsmall)

    ## @annotation

    annotation(CCLEsmall)

    annotation(CCLEsmall) <- annotation(CCLEsmall)

    dateCreated(CCLEsmall)

    ## dateCreated
    dateCreated(CCLEsmall) <- date()

    name(CCLEsmall)

    name(CCLEsmall) <- 'new_name'

    cellInfo(CCLEsmall) <- cellInfo(CCLEsmall)

    cellNames(CCLEsmall)

    cellNames(CCLEsmall) <- cellNames(CCLEsmall)

    ## curation
    curation(CCLEsmall)

    curation(CCLEsmall) <- curation(CCLEsmall)

    datasetType(CCLEsmall)

    datasetType(CCLEsmall) <- 'both'

    # No assay specified
    molecularProfiles(CCLEsmall, 'rna') <- molecularProfiles(CCLEsmall, 'rna')

    # Specific assay
    molecularProfiles(CCLEsmall, 'rna', 'exprs') <-
        molecularProfiles(CCLEsmall, 'rna', 'exprs')

    featureInfo(CCLEsmall, 'rna')

    featureInfo(CCLEsmall, 'rna') <- featureInfo(CCLEsmall, 'rna')

    phenoInfo(CCLEsmall, 'rna')

    phenoInfo(CCLEsmall, 'rna') <- phenoInfo(CCLEsmall, 'rna')

    fNames(CCLEsmall, 'rna')

    fNames(CCLEsmall, 'rna') <- fNames(CCLEsmall, 'rna')

    mDataNames(CCLEsmall)

    mDataNames(CCLEsmall) <- mDataNames(CCLEsmall)

    molecularProfilesSlot(CCLEsmall)

    molecularProfilesSlot(CCLEsmall) <- molecularProfilesSlot(CCLEsmall)

    sensitivityInfo(CCLEsmall)

    sensitivityInfo(CCLEsmall) <- sensitivityInfo(CCLEsmall)

    sensitivityMeasures(CCLEsmall) <- sensitivityMeasures(CCLEsmall)

    sensitivityMeasures(CCLEsmall) <- sensitivityMeasures(CCLEsmall)

    sensitivityProfiles(CCLEsmall)

    sensitivityProfiles(CCLEsmall) <- sensitivityProfiles(CCLEsmall)

    head(sensitivityRaw(CCLEsmall))

    sensitivityRaw(CCLEsmall) <- sensitivityRaw(CCLEsmall)

    sensitivitySlot(CCLEsmall)

    sensitivitySlot(CCLEsmall) <- sensitivitySlot(CCLEsmall)

    sensNumber(CCLEsmall)

    sensNumber(CCLEsmall) <- sensNumber(CCLEsmall)

    pertNumber(CCLEsmall)

    pertNumber(CCLEsmall) <- pertNumber(CCLEsmall)

[Package PharmacoGx version 2.4.0 Index]