MultiAssayExperiment-class: An integrative multi-assay class for experiment data

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

Description

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.

Usage

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## 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, ...)

Arguments

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

Details

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

Value

A MultiAssayExperiment object

Methods (by generic)

Slots

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

colData

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.

ExperimentList

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

sampleMap

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".

See Also

MultiAssayExperiment-methods for slot modifying methods

Examples

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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)

vjcitn/MultiAssayExperiment documentation built on Dec. 30, 2017, 4:33 a.m.