# Software for the integration of multi-omics experiments in Bioconductor

## Documentation for package ‘MultiAssayExperiment’ version 1.30.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E G H I L M N P R S U W misc

MultiAssayExperiment-package | MultiAssayExperiment: Build an integrative multi-assay container

## -- A --

anyReplicated | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
anyReplicated-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
assay-method | ExperimentList - A container for multi-experiment data
assay-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
assays-method | ExperimentList - A container for multi-experiment data
assays-method | MultiAssayExperiment - An integrative multi-assay class for experiment data

## -- C --

c-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
coerce-ExperimentList | ExperimentList - A container for multi-experiment data
coerce-method | ExperimentList - A container for multi-experiment data
coerce-method | MatchedAssayExperiment - A matched-samples MultiAssayExperiment class
coerce-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
coerce-MultiAssayExperiment | MultiAssayExperiment - An integrative multi-assay class for experiment data
colData-method | Accessing and modifying information in MultiAssayExperiment
colData<--method | Accessing and modifying information in MultiAssayExperiment
colnames-method | ExperimentList - A container for multi-experiment data
colnames<--method | Accessing and modifying information in MultiAssayExperiment
complete.cases-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment

## -- D --

DataFrame | Objects exported from other packages
dimnames-method | ExperimentList - A container for multi-experiment data
dimnames-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
drops | Accessing and modifying information in MultiAssayExperiment
drops-method | Accessing and modifying information in MultiAssayExperiment
drops<- | Accessing and modifying information in MultiAssayExperiment
drops<--method | Accessing and modifying information in MultiAssayExperiment

## -- E --

ExperimentList | Represent multiple experiments as a List-derivative 'ExperimentList'
ExperimentList-class | ExperimentList - A container for multi-experiment data
experiments | Accessing and modifying information in MultiAssayExperiment
experiments-method | Accessing and modifying information in MultiAssayExperiment
experiments<- | Accessing and modifying information in MultiAssayExperiment
experiments<--method | Accessing and modifying information in MultiAssayExperiment
exportClass | MultiAssayExperiment - An integrative multi-assay class for experiment data
exportClass-method | MultiAssayExperiment - An integrative multi-assay class for experiment data

## -- G --

getWithColData | A group of helper functions for manipulating and cleaning a MultiAssayExperiment

## -- H --

hasAssay | Checking assay method for any class
hasRowRanges | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
hasRowRanges-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
HDF5MultiAssayExperiment | Save a MultiAssayExperiment class object to HDF5 and Rds files

## -- I --

intersectColumns | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
intersectRows | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
isEmpty-method | ExperimentList - A container for multi-experiment data
isEmpty-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment

## -- L --

length-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
listToMap | Convert map from data.frame or DataFrame to list and vice versa
loadHDF5MultiAssayExperiment | Save a MultiAssayExperiment class object to HDF5 and Rds files
longFormat | A group of helper functions for manipulating and cleaning a MultiAssayExperiment

## -- M --

makeHitList | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
makeMatchList | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
mapToList | Convert map from data.frame or DataFrame to list and vice versa
MatchedAssayExperiment | MatchedAssayExperiment - A matched-samples MultiAssayExperiment class
MatchedAssayExperiment-class | MatchedAssayExperiment - A matched-samples MultiAssayExperiment class
mergeReplicates | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
mergeReplicates-method | ExperimentList - A container for multi-experiment data
mergeReplicates-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
metadata-method | Accessing and modifying information in MultiAssayExperiment
metadata<--method | Accessing and modifying information in MultiAssayExperiment
miniACC | Adrenocortical Carcinoma (ACC) MultiAssayExperiment
MultiAssayExperiment | Construct an integrative representation of multi-omic data with 'MultiAssayExperiment'
MultiAssayExperiment-class | MultiAssayExperiment - An integrative multi-assay class for experiment data
MultiAssayExperiment-helpers | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
MultiAssayExperiment-methods | Accessing and modifying information in MultiAssayExperiment
MultiAssayExperimentToMAF | Convert MultiAssayExperiment to MAF class

## -- N --

names-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
names<--method | Accessing and modifying information in MultiAssayExperiment

## -- P --

prepMultiAssay | Prepare a 'MultiAssayExperiment' instance

## -- R --

reexports | Objects exported from other packages
renameColname | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
renamePrimary | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
replicated | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
replicated-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
replicates | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
replicates-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
rownames-method | ExperimentList - A container for multi-experiment data

## -- S --

sampleMap | Accessing and modifying information in MultiAssayExperiment
sampleMap-method | Accessing and modifying information in MultiAssayExperiment
sampleMap<- | Accessing and modifying information in MultiAssayExperiment
sampleMap<--method | Accessing and modifying information in MultiAssayExperiment
saveHDF5MultiAssayExperiment | Save a MultiAssayExperiment class object to HDF5 and Rds files
show-method | ExperimentList - A container for multi-experiment data
show-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
showReplicated | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
showReplicated-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
splitAssays | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
splitAssays-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
subset | Subsetting a MultiAssayExperiment object
subsetBy | Subsetting a MultiAssayExperiment object
subsetByAssay | Subsetting a MultiAssayExperiment object
subsetByAssay-method | Subsetting a MultiAssayExperiment object
subsetByColData | Subsetting a MultiAssayExperiment object
subsetByColData-method | Subsetting a MultiAssayExperiment object
subsetByColumn | Subsetting a MultiAssayExperiment object
subsetByColumn-method | Subsetting a MultiAssayExperiment object
subsetByRow | Subsetting a MultiAssayExperiment object
subsetByRow-method | Subsetting a MultiAssayExperiment object

## -- U --

updateObject-method | MultiAssayExperiment - An integrative multi-assay class for experiment data
upsetSamples | Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in 'UpSetR'

## -- W --

wideFormat | A group of helper functions for manipulating and cleaning a MultiAssayExperiment

## -- misc --

$-method | Accessing and modifying information in MultiAssayExperiment
$<--method | Accessing and modifying information in MultiAssayExperiment
[-method | Subsetting a MultiAssayExperiment object
[<--method | Subsetting a MultiAssayExperiment object
[[-method | Subsetting a MultiAssayExperiment object
[[<--method | Subsetting a MultiAssayExperiment object