Package: MultiAssayExperiment 1.39.0

Summary of the MultiAssayExperiment API | API Overview | Constructors | Accessors | Subsetting | Management | Reshaping | Combining | Coercion | Export | Notes

Installation | Citing MultiAssayExperiment | A Brief Description | Choosing the appropriate data structure | Overview of the MultiAssayExperiment class | Components of the MultiAssayExperiment | ExperimentList: experimental data | Class requirements within ExperimentList container | colData: primary data | colData slot requirements | Note on the flexibility of the DataFrame | sampleMap: relating colData to multiple assays | sampleMap structure | Instances where sampleMap isn't provided | metadata | Creating a MultiAssayExperiment object: a rich example | Create toy datasets demonstrating all supported data types | sampleMap creation | Experimental data as a list() | Creation of the MultiAssayExperiment class object | Helper function to create a MultiAssayExperiment object | Helper functions to create Bioconductor classes from raw data | Integrated subsetting across experiments | Subsetting by square bracket [ | Subsetting by character, integer, and logical | the "drop" argument | More on subsetting by columns | Subsetting assays | Subsetting rows (features) by IDs, integers, or logicals | Subsetting rows (features) by GenomicRanges | Subsetting is endomorphic | Double-bracket subsetting to select experiments | Helpers for data clean-up and management | complete.cases | replicated | intersectRows | intersectColumns | mergeReplicates | combine c | Extractor functions | getWithColData | longForm & wideFormat | assay / assays | The Cancer Genome Atlas and MultiAssayExperiment | Dimension names: rownames and colnames | Requirements for support of additional data classes | Application Programming Interface (API) | Methods for MultiAssayExperiment | sessionInfo() | References

Integrating an HDF5 backend for MultiAssayExperiment | Dependencies | HDF5Array and DelayedArray Constructor | Writing to a file with dimnames | Importing HDF5 files | Using a DelayedMatrix with MultiAssayExperiment | SummarizedExperiment with DelayedMatrix backend | Session info

Component slots | colData - information on biological units | ExperimentList - experiment data | sampleMap - relationship graph | metadata | Subsetting | Single bracket [ | Subsetting by genomic ranges | Double bracket [[ | Patients with complete data | Row names that are common across assays | Extraction | assay and assays | Summary of slots and accessors | Transformation / reshaping | longForm | wideFormat | MultiAssayExperiment class construction and concatenation | MultiAssayExperiment constructor function | prepMultiAssay - Constructor function helper | c - concatenate to MultiAssayExperiment | Examples | UpsetR "Venn" diagram | Kaplan-meier plot stratified by a clinical variable | Multivariate Cox regression including RNA-seq, copy number, and pathology | Session info