MultiAssayExperiment-methods: Accessing/modifying slot information

In vjcitn/MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

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,ExperimentList'
experiments(object) <- value

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

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

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

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

Arguments

x	A MultiAssayExperiment object
...	Argument not in use
object	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(myMultiAssayExperiment)

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

## Access the ExperimentList
experiments(myMultiAssayExperiment)

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

## Access the metadata
metadata(myMultiAssayExperiment)

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

## Access the colData
colData(myMultiAssayExperiment)

## Access a column in colData
myMultiAssayExperiment$age

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

vjcitn/MultiAssayExperiment documentation built on May 3, 2019, 6:13 p.m.