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Convert cheatsheet from pdf to Rmd
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‎DESCRIPTION‎

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h5mread,
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knitr,
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maftools,
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R.rsp,
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RaggedExperiment,
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reshape2,
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rmarkdown,
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survival,
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survminer,
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testthat,
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UpSetR
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VignetteBuilder:
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knitr,
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R.rsp
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VignetteBuilder: knitr
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biocViews: Infrastructure, DataRepresentation
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Encoding: UTF-8
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RoxygenNote: 7.3.2

‎vignettes/MultiAssayExperiment_cheatsheet.Rmd‎

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---
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title: "MultiAssayExperiment Cheatsheet"
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author: "MultiAssay Special Interest Group"
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date: "`r format(Sys.time(), '%B %d, %Y')`"
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vignette: >
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%\VignetteEngine{knitr::rmarkdown}
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%\VignetteIndexEntry{MultiAssayExperiment Cheatsheet}
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%\VignetteEncoding{UTF-8}
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output:
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BiocStyle::html_document:
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number_sections: false
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toc: false
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---
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# Summary of the MultiAssayExperiment API
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Updated from Ramos et al., *Cancer Research* 2017; DOI:
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[10.1158/0008-5472.CAN-17-0344](https://doi.org/10.1158/0008-5472.CAN-17-0344)
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## API Overview
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### Constructors
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| Function | Description | Returned Class |
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|:-----------------------|:----------------------------------------------|:-----------------------|
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| `MultiAssayExperiment` | Create a MultiAssayExperiment object | MultiAssayExperiment |
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| `ExperimentList` | Create an ExperimentList from a List or list | ExperimentList |
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### Accessors
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| Function | Description | Returned Class |
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|:-----------------|:----------------------------------------------------------|:-----------------|
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| `colData` | Get or set data that describe patients / biological units | DataFrame |
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| `experiments` | Get or set the list of experimental data objects | ExperimentList |
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| `assays` | Get the list of experimental numeric matrices | SimpleList |
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| `assay` | Get the first experimental numeric matrix | matrix, matrix-like |
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| `sampleMap` | Get or set the map relating observations to subjects | DataFrame |
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| `metadata` | Get or set additional data descriptions | list |
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| `rownames` | Get row names for all experiments | CharacterList |
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| `colnames` | Get column names for all experiments | CharacterList |
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| `getWithColData` | Extract a single assay with whole or assay colData | (varies) |
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### Subsetting
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| Syntax | Description | Returned Class |
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|:-----------------|:-------------------------------------------|:-----------------------|
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| `mae[i, j, k]` | Get rows, columns, and/or experiments | MultiAssayExperiment |
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| `mae[i,,]` | -- `i:` GRanges, character, integer, etc. | MultiAssayExperiment |
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| `mae[,j,]` | -- `j:` character, integer, logical, etc. | MultiAssayExperiment |
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| `mae[,,k]` | -- `k:` character, integer, logical | MultiAssayExperiment |
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| `mae[[n]]` | Get/set object from experiments | (varies) |
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| `mae$column` | Get/set `colData` column vector | (varies) |
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| `getWithColData(mae, k)` | Extract a single assay with colData; k: char, int | (varies) |
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| `subsetByColData(mae, ..)` | Select rows from colData and re-harmonize data | MultiAssayExperiment |
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### Management
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| Function | Description | Returned Class |
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|:---------------------|:-------------------------------------------------------------|:-----------------------|
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| `prepMultiAssay` | Troubleshoot constructor problems constructing class | list |
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| `complete.cases` | Identify subjects with complete data | logical vector |
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| `replicated` | Identify replicate observations per experiment | list of LogicalLists |
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| `anyReplicated` | Whether any replicate observations exist | logical vector |
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| `showReplicated` | Show actual technical replicate obs. in assay | list of CharacterLists |
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| `mergeReplicates` | Merge replicate observations within each experiment | MultiAssayExperiment |
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| `intersectRows` | Features present in all experiments | MultiAssayExperiment |
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| `intersectColumns` | Subjects with data in all experiments | MultiAssayExperiment |
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| `renameColname` | Rename the assay column names for a single assay | MultiAssayExperiment |
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| `renamePrimary` | Rename the colData rownames | MultiAssayExperiment |
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| `splitAssay` | Separate columns from assays using a 'hitList' of logical vectors | MultiAssayExperiment |
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| `makeHitList` | Create a 'hitList' list based on patterns for matching assay colnames | list |
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### Reshaping
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| Function | Description | Returned Class |
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|:-----------------|:-----------------------------------------------------|:-----------------|
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| `longFormat` | Long tidy DataFrame with optional `colData` columns | DataFrame |
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| `wideFormat` | Wide format, one row per subject | DataFrame |
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### Combining
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| Function | Description | Returned Class |
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|:---------|:-------------------------------------------------|:-----------------------|
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| `c` | Concatenate experiment to MAE | MultiAssayExperiment |
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### Coercion
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| Function | Description | Returned Class |
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|:---------|:-------------------------------------------------|:-----------------------|
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| `MultiAssayExperimentToMAF` | Convert MAE to `MAF` using 'non_syn' and 'syn' assays | maftools::MAF |
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### Export
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| Function | Description | Returned Class |
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|:---------|:-------------------------------------------------|:-----------------------|
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| `exportClass` | Save all data from a MAE to a series of text files ('.csv') | (files) |
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| `saveHDF5MultiAssayExperiment` | Save a MAE in '.h5' and '.rds' formats similar to `HDF5Array::saveHDF5SummarizedExperiment` | (files) |
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---
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## Notes
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- **assay**: Procedure for measuring biological activity (e.g., RNA-seq).
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- **experiment**: Application of an assay to a sample set.
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- **mae**: A `MultiAssayExperiment` object.
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- **subject**: Patient, cell line, or other biological unit.
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- **observation**: Results of an assay (e.g., gene expression).
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- **features**: Measurement units labeled by row names or genomic ranges.
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- `duplicated()` was deprecated in Bioconductor 3.7 and replaced by `replicated()`.
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‎vignettes/MultiAssayExperiment_cheatsheet.pdf‎

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‎vignettes/MultiAssayExperiment_cheatsheet.pdf.asis‎

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