Software for the integration of multi-omics experiments in Bioconductor

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Documentation for package ‘MultiAssayExperiment’ version 1.24.0

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$-method Accessing and modifying information in MultiAssayExperiment
$<--method Accessing and modifying information in MultiAssayExperiment
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-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
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
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
getWithColData A group of helper functions for manipulating and cleaning a MultiAssayExperiment
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
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
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
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
names-method MultiAssayExperiment - An integrative multi-assay class for experiment data
names<--method Accessing and modifying information in MultiAssayExperiment
prepMultiAssay Prepare a 'MultiAssayExperiment' instance
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
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
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
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'
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
[[<--method Subsetting a MultiAssayExperiment object