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

## Documentation for package ‘MultiAssayExperiment’ version 1.2.1

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

## Help Pages

$-method | Accessing/modifying slot information
$<--method | Accessing/modifying slot information
API | Refer to the API documentation
assay-method | A container for multi-experiment data
assay-method | An integrative multi-assay class for experiment data
assay-method | Create a Matrix of score values using a GRanges or own ranges
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
clusterOn | Check expression of a given feature against clinical variable
colData-method | Accessing/modifying slot information
colData<--method | Accessing/modifying slot information
complete.cases-method | An integrative multi-assay class for experiment data
dim-method | An extension of the GRangesList class
dimnames-method | A container for multi-experiment data
dimnames-method | An integrative multi-assay class for experiment data
dimnames-method | An extension of the GRangesList class
dimnames<--method | An extension of the GRangesList class
disjoin-method | An extension of the GRangesList class
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
ExperimentList-method | 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
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 | An integrative multi-assay class for experiment data
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
longFormat-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
longFormat-method | An extension of the GRangesList class
mapToList | Convert map from data.frame or DataFrame to list and vice versa
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
mergeReplicates-method | An extension of the GRangesList class
metadata-method | Accessing/modifying slot information
metadata<--method | Accessing/modifying slot information
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
pData-method | Accessing/modifying slot information
pData<--method | Accessing/modifying slot information
prepMultiAssay | Prepare a 'MultiAssayExperiment' instance
RangedRaggedAssay | Create a RangedRaggedAssay
RangedRaggedAssay-class | An extension of the GRangesList class
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
show-method | An extension of the GRangesList class
subsetByAssay | Subset 'MultiAssayExperiment' object by Assay type
subsetByAssay-method | Subset 'MultiAssayExperiment' object by Assay type
subsetByColData | Subset 'MultiAssayExperiment' object by 'colData' rows
subsetByColData-method | Subset 'MultiAssayExperiment' object by 'colData' rows
subsetByColumn | Subset 'MultiAssayExperiment' object
subsetByColumn-method | Subset 'MultiAssayExperiment' object
subsetByRow | Subset 'MultiAssayExperiment' object by Feature
subsetByRow-method | Subset 'MultiAssayExperiment' object by Feature
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
wideFormat-method | A group of helper functions for manipulating and cleaning a MultiAssayExperiment
[-method | An integrative multi-assay class for experiment data
[-method | An extension of the GRangesList class
[[-method | Accessing/modifying slot information
[[<--method | Accessing/modifying slot information