MultiAssayExperiment-class: MultiAssayExperiment - An integrative multi-assay class for...

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

MultiAssayExperiment - An integrative multi-assay class for experiment data

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

## 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'
exportClass(
  object,
  dir = tempdir(),
  fmt,
  ext,
  match = FALSE,
  verbose = TRUE,
  ...
)

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

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

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

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

Arguments

object, x	A MultiAssayExperiment object
...	Additional arguments for supporting functions. See details.
verbose	logical(1) Whether to print additional information (default TRUE)
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). If using a character input, the name must match exactly.
dir	character(1) A directory for saving exported data (default: tempdir())
fmt	character(1) or function() Either a format character atomic as supported by write.table either ('csv', or 'tsv') or a function whose first two arguments are 'object to save' and 'file location'
ext	character(1) A file extension supported by the format argument
match	logical(1) Whether to coerce the current object to a 'MatchedAssayExperiment' object (default: FALSE)
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.

• subsetting [: additional arguments sent to findOverlaps.

• mergeReplicates: used to specify arguments for the simplify functional argument

• assay: may contain withDimnames, which is forwarded to assays

• combining c: compatible MultiAssayExperiment classes passed on to the ExperimentList constructor, can be a list, List, or a series of named arguments. See the examples below.

Value

A MultiAssayExperiment object

Methods (by generic)

• show(MultiAssayExperiment): Show method for a MultiAssayExperiment

• length(MultiAssayExperiment): Get the length of ExperimentList

• names(MultiAssayExperiment): Get the names of the ExperimentList

• updateObject(MultiAssayExperiment): Update old serialized MultiAssayExperiment objects to new API

• dimnames(MultiAssayExperiment): Get the dimension names for a MultiAssayExperiment object

• c(MultiAssayExperiment): Add a supported data class to the ExperimentList

• exportClass(MultiAssayExperiment): Export data from class to a series of text files

• assays(MultiAssayExperiment): Obtain a SimpleList of assay data for all available experiments in the object

• assay(x = MultiAssayExperiment, i = missing): Convenience function for extracting the assay of the first element (default) in the ExperimentList. A numeric or character index can also be provided

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. The standard column names of the sampleMap are "assay", "primary", and "colname". Note that the "assay" column is a factor corresponding to the names of each experiment in the ExperimentList. In the case where these names do not match between the sampleMap and the experiments, the documented experiments in the sampleMap take precedence and experiments are dropped by the harmonization procedure. The constructor function will generate a sampleMap in the case where it is not provided and this method may be a 'safer' alternative for creating the MultiAssayExperiment (so long as the rownames are identical in the colData, if provided). An empty sampleMap may produce empty experiments if the levels of the "assay" factor in the sampleMap do not match the names in the ExperimentList.

coercion

Convert a list or S4 List to a MultiAssayExperiment object using the methods::as function.

In the following example, x is either a list or List:

as(x, "MultiAssayExperiment")

Convert a MultiAssayExperiment to MAF class object using the methods::as function.

In the following example, x is a MultiAssayExperiment:

MultiAssayExperimentToMAF(x)

See Also

MultiAssayExperiment-methods for slot modifying methods, MultiAssayExperiment API

Examples

example("MultiAssayExperiment")

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

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

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

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

example("MultiAssayExperiment")

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

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

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

## Add experiment using experiment name in mapFrom
c(mae, RNASeqGeneV2 = test2, mapFrom = "RNASeqGene")

waldronlab/MultiAssayExperiment documentation built on Dec. 24, 2024, 8:10 a.m.