Package index • 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

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

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

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

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

Compatibility with other Bioconductor packages

saveHDF5MultiAssayExperiment() loadHDF5MultiAssayExperiment(): Save a MultiAssayExperiment class object to HDF5 and Rds files

Other package information and data

MultiAssayExperiment-package: MultiAssayExperiment: Build an integrative multi-assay container