multiomeR Implementation
1 Introduction
Use this book to trace a result back to its code or change how multiomeR works. For installation, configuration, execution, and output inspection, start with the user manual. You do not need to read this book to run the demo.
Use this book when you need to trace a configuration value into mapped targets, understand how the simplified graph views relate to the real {targets} graph, or decide where an implementation change belongs.
1.1 Where to start
For a first implementation pass:
- Read Reading the graph views and follow its configuration-to-target trace.
- Open the main pipeline graph for the modality or checkpoint you plan to change.
- Use Implementation conventions to understand the relevant manifest, mapping, symbol, tag, and runtime contracts.
- Read Background and design philosophy when you need the rationale for the editable-workflow design.
The differential analyses and genetic enrichment chapters cover the optional module graphs.
1.2 Common entry points
| Change | Start with |
|---|---|
| Add or revise a YAML parameter | cfg_pipeline_parameters.tsv, then the owning config reader or target. |
| Change GEM well preprocessing | _targets.R mapping plus extra_targets/per_GEM_well_targets.R. |
| Change aggregation GEX, ATAC, or WNN processing | The corresponding graph section and extra_targets/*_targets.R file. |
| Inspect existing review selections | [checkpoint:<name>] description tags and the numbered QC review guide. |
| Add a graph-visible target | Existing [part_of_graph:<graph_id>] tags and graph-pruning rules. |
| Change resource routing | crew_controllers.R, packages/multiomeRCore/R/resource_helpers.R, and the runtime bootstrap convention. |
If you are trying to run multiomeR rather than modify it, start with the main manual.