MultiAssayExperiment-methods {MultiAssayExperiment} | R Documentation

## Accessing and modifying information in MultiAssayExperiment

### Description

A set of accessor and setter generic functions to extract either the `sampleMap`, the `ExperimentList`, `colData`, or `metadata` slots of a `MultiAssayExperiment` object

### Usage

    ## S4 method for signature 'MultiAssayExperiment'
    sampleMap(x)

    ## S4 method for signature 'MultiAssayExperiment'
    experiments(x)

    ## S4 method for signature 'MultiAssayExperiment'
    colData(x, ...)

    ## S4 method for signature 'MultiAssayExperiment'
    metadata(x)

    ## S4 replacement method for signature 'MultiAssayExperiment,DataFrame'
    sampleMap(object) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment,ANY'
    sampleMap(object) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment,ExperimentList'
    experiments(object) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment,List'
    experiments(object) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment,DataFrame'
    colData(x) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment,ANY'
    colData(x) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment'
    metadata(x, ...) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment'
    x$name <- value

    ## S4 replacement method for signature 'MultiAssayExperiment'
    names(x) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment,List'
    colnames(x) <- value

    ## S4 replacement method for signature 'MultiAssayExperiment,list'
    colnames(x) <- value

    ## S4 method for signature 'MultiAssayExperiment'
    x$name

### Arguments

`...` | Argument not in use
`object, x` | A `MultiAssayExperiment` object
`value` | See details.
`name` | A column in `colData`

### Value

Accessors: Either a `sampleMap`, `ExperimentList`, or `DataFrame` object

Setters: A `MultiAssayExperiment` object

### Accessors

Eponymous names for accessing `MultiAssayExperiment` slots with the exception of the ExperimentList accessor named `experiments`.

- colData: Access the `colData` slot

- sampleMap: Access the `sampleMap` slot

- experiments: Access the ExperimentList slot

- '[[': Access the ExperimentList slot

- '$': Access a column in `colData`

### Setters

Setter method values (i.e., '`function(x) <- value`'):

- experiments<-: An `ExperimentList` object containing experiment data of supported classes

- sampleMap<-: A `DataFrame` object relating samples to biological units and assays

- colData<-: A `DataFrame` object describing the biological units

- metadata<-: A `list` object of metadata

- '[[<-': Equivalent to the `experiments<-` setter method for convenience

- '$<-': A vector to replace the indicated column in `colData`

### Examples

    ## Load example MultiAssayExperiment
    example(MultiAssayExperiment)

    ## Access the sampleMap
    sampleMap(mae)

    ## Replacement method for a MultiAssayExperiment sampleMap
    sampleMap(mae) <- S4Vectors::DataFrame()

    ## Access the ExperimentList
    experiments(mae)

    ## Replace with an empty ExperimentList
    experiments(mae) <- ExperimentList()

    ## Access the metadata
    metadata(mae)

    ## Replace metadata with a list
    metadata(mae) <- list(runDate =
        format(Sys.time(), "%B %d, %Y"))

    ## Access the colData
    colData(mae)

    ## Access a column in colData
    mae$age

    ## Replace a column in colData
    mae$age <- mae$age + 1

[Package MultiAssayExperiment version 1.20.0 Index]