MultiAssayExperiment-methods: Accessing and modifying information in MultiAssayExperiment

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

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'
drops(x)

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

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

drops(x, ...) <- 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'
drops(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

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

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

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

• drops: Get a vector of dropped ExperimentList names

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

• ⁠drops<-⁠: Trace ExperimentList names that have been removed

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

waldronlab/MultiAssayExperiment documentation built on Nov. 4, 2024, 7:51 a.m.