MultiAssayExperiment-class: An integrative multi-assay class for experiment data
In vjcitn/MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

Description Usage Arguments Details Value Methods (by generic) Slots colData ExperimentList sampleMap See Also Examples

The MultiAssayExperiment class can be used to manage results of diverse assays on a collection of specimen. Currently, the class can handle assays that are organized instances of SummarizedExperiment, ExpressionSet, matrix, RaggedExperiment (inherits from GRangesList), and RangedVcfStack. Create new MultiAssayExperiment instances with the homonymous constructor, minimally with the argument ExperimentList, potentially also with the arguments colData (see section below) and sampleMap.

## S4 method for signature 'MultiAssayExperiment'
show(object)

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

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

## S4 method for signature 'MultiAssayExperiment'
updateObject(object, ..., verbose = FALSE)

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

## S4 method for signature 'MultiAssayExperiment'
c(x, ..., sampleMap = NULL, mapFrom = NULL)

## S4 method for signature 'MultiAssayExperiment'
assays(x, ..., withDimnames = TRUE)

## S4 method for signature 'MultiAssayExperiment,missing'
assay(x, i, ...)

## S4 method for signature 'MultiAssayExperiment,numeric'
assay(x, i, ...)

## S4 method for signature 'MultiAssayExperiment,character'
assay(x, i, ...)

`object`	A `MultiAssayExperiment` object
`x`	A `MultiAssayExperiment` object
`...`	Additional arguments for supporting functions. See details.
`verbose`	logical (default FALSE) whether to print extra messages
`sampleMap`	`c` method: a `sampleMap` `list` or `DataFrame` to guide merge
`mapFrom`	Either a `logical`, `character`, or `integer` vector indicating the experiment(s) that have an identical colname order as the experiment input(s)
`withDimnames`	logical (default TRUE) whether to return dimension names included in the object
`i`	An integer or character scalar indicating the assay to return

The dots (...) argument allows the user to specify additional arguments in several instances. When subsetting ([) a MultiAssayExperiment, the dots allow for additional arguments to be sent to findOverlaps. When using the mergeReplicates method, the dots are used to specify arguments for the supplied simplify argument and function. When using the assay method. When using c method to add experiments to a MultiAssayExperiment, the dots allow extra data classes compatible with the MultiAssayExperiment API. See the MultiAssayExperiment API

A MultiAssayExperiment object

show: Show method for a MultiAssayExperiment
length: Get the length of ExperimentList
names: Get the names of the ExperimentList
updateObject: Update old serialized MultiAssayExperiment objects to new API
dimnames: Get the dimension names for a MultiAssayExperiment object
c: Add an element to the ExperimentList data slot
assays: Obtain a SimpleList of assay data for all available experiments in the object
assay: Convenience function for extracting the assay of the first element in the ExperimentList
assay: Obtain the specified assay from the MultiAssayExperiment with a numeric index
assay: Get the specified assay from the MultiAssayExperiment with a character index

ExperimentList: A ExperimentList class object for each assay dataset
colData: A DataFrame of all clinical/specimen data available across experiments
sampleMap: A DataFrame of translatable identifiers of samples and participants
metadata: Additional data describing the MultiAssayExperiment object
drops: A metadata list of dropped information

The colData slot is a collection of primary specimen data valid across all experiments. This slot is strictly of class DataFrame but arguments for the constructor function allow arguments to be of class data.frame and subsequently coerced.

The ExperimentList slot is designed to contain results from each experiment/assay. It contains a SimpleList.

The sampleMap contains a DataFrame of translatable identifiers of samples and participants or biological units. Standard column names of the sampleMap are "assay", "primary", and "colname".

MultiAssayExperiment-methods for slot modifying methods

example("MultiAssayExperiment")

## Subsetting
# Rows (i) Rows/Features in each experiment
myMultiAssayExperiment[1, , ]
myMultiAssayExperiment[c(TRUE, FALSE), , ]

# Columns (j) Rows in colData
myMultiAssayExperiment[, rownames(colData(myMultiAssayExperiment))[3:2],  ]

# Assays (k)
myMultiAssayExperiment[, , "Affy"]

## Complete cases (returns logical vector)
completes <- complete.cases(myMultiAssayExperiment)
compMAE <- myMultiAssayExperiment[, completes, ]
compMAE
colData(compMAE)

example("MultiAssayExperiment")

## Add an experiment
test1 <- myMultiAssayExperiment[[1L]]
colnames(test1) <- rownames(colData(myMultiAssayExperiment))

## Combine current MultiAssayExperiment with additional experiment
## (no sampleMap)
c(myMultiAssayExperiment, newExperiment = test1)

test2 <- myMultiAssayExperiment[[1L]]
c(myMultiAssayExperiment, newExp = test2, mapFrom = 3L)