# Software for the integration of multi-omics experiments in Bioconductor

## Documentation for package ‘MultiAssayExperiment’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

$-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 The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

assay-method | MultiAssayExperiment - An integrative multi-assay class for experiment data

assays-method

ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

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 The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

coerce-method

ExperimentList - A container for multi-experiment data The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

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 | 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 The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

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 The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

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 The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

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 The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

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
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 The 'ExperimentList' class is a container that builds on the 'SimpleList' with additional checks for consistency in experiment names and length. It contains a 'SimpleList' of experiments with sample identifiers. One element present per experiment performed. Convert from 'SimpleList' or 'list' to the multi-experiment data container. When using the *mergeReplicates* method, additional arguments are passed to the given 'simplify' function argument (e.g., na.rm = TRUE)

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