Software for the Integration of Multi-omics Experiments in Bioconductor

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Documentation for package ‘MultiAssayExperiment’ version 1.4.9

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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 (DEFUNCT)
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 (DEFUNCT)
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 (DEFUNCT)
dimnames<--method An extension of the GRangesList class (DEFUNCT)
disjoin-method An extension of the GRangesList class (DEFUNCT)
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 (DEFUNCT)
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
mergeReplicates-method An extension of the GRangesList class (DEFUNCT)
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
pData-method Accessing/modifying slot information
pData<--method Accessing/modifying slot information
prepMultiAssay Prepare a 'MultiAssayExperiment' instance
RangedRaggedAssay Create a RangedRaggedAssay (DEFUNCT)
RangedRaggedAssay-class An extension of the GRangesList class (DEFUNCT)
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 (DEFUNCT)
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
subsetByColumns Subsetting a MultiAssayExperiment object
subsetByRow Subsetting a MultiAssayExperiment object
subsetByRow-method Subsetting a MultiAssayExperiment object
subsetByRows 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
wideFormat-method A group of helper functions for manipulating and cleaning a MultiAssayExperiment
[-method An extension of the GRangesList class (DEFUNCT)
[-method Subsetting a MultiAssayExperiment object
[[-method Subsetting a MultiAssayExperiment object
[[<--method Subsetting a MultiAssayExperiment object