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>) drops(<MultiAssayExperiment>) `sampleMap<-`(<MultiAssayExperiment>,<DataFrame>) `sampleMap<-`(<MultiAssayExperiment>,<ANY>) `drops<-`() `experiments<-`(<MultiAssayExperiment>,<ExperimentList>) `experiments<-`(<MultiAssayExperiment>,<List>) `colData<-`(<MultiAssayExperiment>,<DataFrame>) `colData<-`(<MultiAssayExperiment>,<ANY>) `$<-`(<MultiAssayExperiment>) `names<-`(<MultiAssayExperiment>) `colnames<-`(<MultiAssayExperiment>,<List>) `colnames<-`(<MultiAssayExperiment>,<list>) `$`(<MultiAssayExperiment>) metadata(<MultiAssayExperiment>) `metadata<-`(<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 Formats

Compatibility with other Bioconductor packages

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