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>)
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>)
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
MultiAssayExperiment
ExperimentList()
Represent multiple experiments as a List-derivative ExperimentList
ExperimentList
Discover content within MultiAssayExperiment
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>)
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
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>)
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()
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
UpSetR
listToMap() mapToList()
listToMap()
mapToList()
Convert map from data.frame or DataFrame to list and vice versa
prepMultiAssay()
Prepare a MultiAssayExperiment instance
Working with HDF5Array and maftools
saveHDF5MultiAssayExperiment() loadHDF5MultiAssayExperiment()
saveHDF5MultiAssayExperiment()
loadHDF5MultiAssayExperiment()
Save a MultiAssayExperiment class object to HDF5 and Rds files
MultiAssayExperimentToMAF()
Convert MultiAssayExperiment to MAF class
Other package information and data
MultiAssayExperiment: Build an integrative multi-assay container
hasAssay()
Checking assay method for any class
reexports DataFrame
reexports
DataFrame
Objects exported from other packages
miniACC
Adrenocortical Carcinoma (ACC) MultiAssayExperiment