# Create Classes and Functions for Managing Multiple Assays on Sets of Samples

## Documentation for package ‘MultiAssayExperiment’ version 1.0.1

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

## Help Pages

MultiAssayExperiment-package | MultiAssayExperiment: Build an integrative multi-assay container
$-method | An integrative MultiAssay class for experiment data
$<--method | An integrative MultiAssay class for experiment data
.ExperimentList | A container for multi-experiment data
.RangedRaggedAssay | An extension of the GRangesList class
API | Refer to the API documentation
assay-method | A container for multi-experiment data
assay-method | An integrative MultiAssay class for experiment data
assay-method | Create a Matrix of score values using a GRanges or own ranges
complete.cases-method | An integrative MultiAssay class for experiment data
dim-method | An extension of the GRangesList class
dimnames-method | A container for multi-experiment data
dimnames-method | An integrative MultiAssay class for experiment data
dimnames-method | An extension of the GRangesList class
dimnames<--method | An extension of the GRangesList class
ExperimentList | experiment Acessor function for the 'ExperimentList' slot of a 'MultiAssayExperiment' object
ExperimentList-class | A container for multi-experiment data
ExperimentList-method | A container for multi-experiment data
experiments | Accessor function for the 'ExperimentList' slot of a 'MultiAssayExperiment' object
experiments-method | An integrative MultiAssay class for experiment data
experiments<- | Replace an 'ExperimentList' slot value with a given 'ExperimentList' class object
experiments<--method | An integrative MultiAssay class for experiment data
getHits | Find hits by class type
getHits-method | An extension of the GRangesList class
getHits-method | Find hits by class type
hasAssay | Checking assay method for any class
isEmpty-method | An integrative MultiAssay class for experiment data
length-method | An integrative MultiAssay class for experiment data
listToMap | Convert map from data.frame or DataFrame to list and vice versa
mapToList | Convert map from data.frame or DataFrame to list and vice versa
metadata-method | An integrative MultiAssay class for experiment data
metadata<--method | An integrative MultiAssay class for experiment data
MultiAssayExperiment | MultiAssayExperiment: Build an integrative multi-assay container
MultiAssayExperiment-class | An integrative MultiAssay class for experiment data
names-method | An integrative MultiAssay class for experiment data
ncol-method | An extension of the GRangesList class
nrow-method | An extension of the GRangesList class
pData-method | An integrative MultiAssay class for experiment data
pData<--method | An integrative MultiAssay class for experiment data
PrepMultiAssay | Prepare a 'MultiAssayExperiment' instance
RangedRaggedAssay | Create a RangedRaggedAssay
RangedRaggedAssay-class | An extension of the GRangesList class
sampleMap | Accessor function for the 'sampleMap' slot of a 'MultiAssayExperiment' object
sampleMap-method | An integrative MultiAssay class for experiment data
sampleMap<- | Replace a slot value with a given 'DataFrame'
sampleMap<--method | An integrative MultiAssay class for experiment data
show-method | A container for multi-experiment data
show-method | An integrative MultiAssay class for experiment data
show-method | An extension of the GRangesList class
subsetByAssay | Subset 'MultiAssayExperiment' object by Assay type
subsetByAssay-method | Subset 'MultiAssayExperiment' object by Assay type
subsetByColumn | Subset 'MultiAssayExperiment' object
subsetByColumn-method | Subset 'MultiAssayExperiment' object
subsetByRow | Subset 'MultiAssayExperiment' object by Feature
subsetByRow-method | Subset 'MultiAssayExperiment' object by Feature
updateObject-method | An integrative MultiAssay class for experiment data
[-method | An integrative MultiAssay class for experiment data
[-method | An extension of the GRangesList class