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

## Documentation for package ‘MultiAssayExperiment’ version 1.8.3

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

## Help Pages

$-method | Accessing/modifying slot information
$<--method | Accessing/modifying slot information
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 | A container for multi-experiment data
assay-method | An integrative multi-assay class for experiment data
assays-method | A container for multi-experiment data
assays-method | An integrative multi-assay class for experiment data
c-method | An integrative multi-assay class for experiment data
coerce | A container for multi-experiment data
coerce-method | A container for multi-experiment data
coerce-method | An integrative and matched-samples class for experiment data
colData-method | Accessing/modifying slot information
colData<--method | Accessing/modifying slot information
complete.cases-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
DataFrame | Objects exported from other packages
dimnames-method | A container for multi-experiment data
dimnames-method | An integrative multi-assay class for experiment data
duplicated | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
duplicated-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
ExperimentList | Construct an 'ExperimentList' object for the 'MultiAssayExperiment' object slot.
ExperimentList-class | A container for multi-experiment data
experiments | Accessing/modifying slot information
experiments-method | Accessing/modifying slot information
experiments<- | Accessing/modifying slot information
experiments<--method | Accessing/modifying slot information
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
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 | A container for multi-experiment data
isEmpty-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
length-method | An integrative multi-assay class for experiment data
listToMap | Convert map from data.frame or DataFrame to list and vice versa
longFormat | 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 | An integrative and matched-samples class for experiment data
MatchedAssayExperiment-class | An integrative and matched-samples class for experiment data
mergeReplicates | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
mergeReplicates-method | A container for multi-experiment data
mergeReplicates-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
metadata-method | Accessing/modifying slot information
metadata<--method | Accessing/modifying slot information
miniACC | Adrenocortical Carcinoma (ACC) MultiAssayExperiment
MultiAssayExperiment | Construct a 'MultiAssayExperiment' object
MultiAssayExperiment-class | An integrative multi-assay class for experiment data
MultiAssayExperiment-helpers | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
MultiAssayExperiment-methods | Accessing/modifying slot information
names-method | An integrative multi-assay class for experiment data
names<--method | Accessing/modifying slot information
prepMultiAssay | Prepare a 'MultiAssayExperiment' instance
reexports | Objects exported from other packages
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
sampleMap | Accessing/modifying slot information
sampleMap-method | Accessing/modifying slot information
sampleMap<- | Accessing/modifying slot information
sampleMap<--method | Accessing/modifying slot information
show-method | A container for multi-experiment data
show-method | An integrative multi-assay class for experiment data
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
updateObject-method | 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'
wideFormat | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
[-method | Subsetting a MultiAssayExperiment object
[[-method | Subsetting a MultiAssayExperiment object
[[<--method | Subsetting a MultiAssayExperiment object