Function reference • MultiAssayExperiment

Classes Exported classes
`show(<ExperimentList>)` `isEmpty(<ExperimentList>)` `dimnames(<ExperimentList>)` `colnames(<ExperimentList>)` `rownames(<ExperimentList>)` `mergeReplicates(<ExperimentList>)` `assay(<ANY>,<missing>)` `assays(<ExperimentList>)` `assay(<ExperimentList>,<missing>)` `assay(<ExperimentList>,<numeric>)` `assay(<ExperimentList>,<character>)`	ExperimentList - A container for multi-experiment data
`show(<MultiAssayExperiment>)` `length(<MultiAssayExperiment>)` `names(<MultiAssayExperiment>)` `updateObject(<MultiAssayExperiment>)` `dimnames(<MultiAssayExperiment>)` `c(<MultiAssayExperiment>)` `exportClass(<MultiAssayExperiment>)` `assays(<MultiAssayExperiment>)` `assay(<MultiAssayExperiment>,<missing>)` `assay(<MultiAssayExperiment>,<numeric>)` `assay(<MultiAssayExperiment>,<character>)`	MultiAssayExperiment - An integrative multi-assay class for experiment data
`MatchedAssayExperiment()`	MatchedAssayExperiment - A matched-samples MultiAssayExperiment class
Constructors Build objects with designated constructor functions
`MultiAssayExperiment()`	Construct an integrative representation of multi-omic data with `MultiAssayExperiment`
`ExperimentList()`	Represent multiple experiments as a List-derivative `ExperimentList`
Methods and Accessors Discover content within MultiAssayExperiment
`show(<MultiAssayExperiment>)` `length(<MultiAssayExperiment>)` `names(<MultiAssayExperiment>)` `updateObject(<MultiAssayExperiment>)` `dimnames(<MultiAssayExperiment>)` `c(<MultiAssayExperiment>)` `exportClass(<MultiAssayExperiment>)` `assays(<MultiAssayExperiment>)` `assay(<MultiAssayExperiment>,<missing>)` `assay(<MultiAssayExperiment>,<numeric>)` `assay(<MultiAssayExperiment>,<character>)`	MultiAssayExperiment - An integrative multi-assay class for experiment data
`sampleMap(<MultiAssayExperiment>)` `experiments(<MultiAssayExperiment>)` `colData(<MultiAssayExperiment>)` `metadata(<MultiAssayExperiment>)` `sampleMap<-`(<MultiAssayExperiment>,<DataFrame>) `sampleMap<-`(<MultiAssayExperiment>,<ANY>) `experiments<-`(<MultiAssayExperiment>,<ExperimentList>) `experiments<-`(<MultiAssayExperiment>,<List>) `colData<-`(<MultiAssayExperiment>,<DataFrame>) `colData<-`(<MultiAssayExperiment>,<ANY>) `metadata<-`(<MultiAssayExperiment>) `$<-`(<MultiAssayExperiment>) `names<-`(<MultiAssayExperiment>) `colnames<-`(<MultiAssayExperiment>,<List>) `colnames<-`(<MultiAssayExperiment>,<list>) `$`(<MultiAssayExperiment>)	Accessing and modifying information in MultiAssayExperiment
Subsetting Easy operations for selecting rows, columns, and/or biological units
`subsetByRow()` `subsetByColData()` `subsetByColumn()` `subsetByAssay()` `[`(<MultiAssayExperiment>,<ANY>,<ANY>,<ANY>) `[[`(<MultiAssayExperiment>,<ANY>,<ANY>) `[[<-`(<MultiAssayExperiment>,<ANY>,<ANY>) `[<-`(<MultiAssayExperiment>,<ANY>,<ANY>,<ANY>)	Subsetting a MultiAssayExperiment object
Management and Reshaping Work with and reshape data
`complete.cases(<MultiAssayExperiment>)` `isEmpty(<MultiAssayExperiment>)` `intersectRows()` `intersectColumns()` `replicated()` `anyReplicated()` `showReplicated()` `replicates()` `mergeReplicates()` `longFormat()` `wideFormat()` `hasRowRanges()` `getWithColData()` `renamePrimary()` `renameColname()` `splitAssays()` `makeHitList()`	A group of helper functions for manipulating and cleaning a MultiAssayExperiment
`upsetSamples()`	Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in `UpSetR`
`listToMap()` `mapToList()`	Convert map from data.frame or DataFrame to list and vice versa
`prepMultiAssay()`	Prepare a `MultiAssayExperiment` instance
External interfaces Working with HDF5Array and maftools
`saveHDF5MultiAssayExperiment()` `loadHDF5MultiAssayExperiment()`	Save a MultiAssayExperiment class object to HDF5 and Rds files
`MultiAssayExperimentToMAF()`	Convert MultiAssayExperiment to MAF class
Misc. Package Docs Other package information and data
	MultiAssayExperiment: Build an integrative multi-assay container
`hasAssay()`	Checking assay method for any class
`reexports` `DataFrame`	Objects exported from other packages
`miniACC`	Adrenocortical Carcinoma (ACC) MultiAssayExperiment

Reference

Classes

Constructors

Methods and Accessors

Subsetting

Management and Reshaping

External interfaces

Misc. Package Docs