Software for the integration of multi-omics experiments in Bioconductor

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Documentation for package ‘MultiAssayExperiment’ version 1.2.1

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$-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