Manual

Manual

Every manual page, grouped by stage of a post-processing project. Step-by-step worked examples are in the Tutorials, and the full argument reference for every function is in the function reference.

Getting started

• Installation: install mrmhub and load it.
• MRMhub overview: the data object, how it moves through a workflow, and the core function groups.

Preparing and running

• Importing analytical data: choosing an importer and the file layout each one expects.
• Importing metadata: attaching sample, feature, and internal-standard annotations.
• Drift and batch correction: correcting signal drift within runs and offsets between batches.
• Isotopic interference correction: the M+2 overlap concepts, the MRM and MS1 derivation levels, and the co-elution requirement.
• Quarto workflows: recording a pipeline as a .qmd notebook, coloured console output, and rendering to HTML, PDF, and Word.

Results and downstream use

• Visualisation functions: RunScatter, PCA, run-sequence, and normalization-QC plots, and exporting figures at a defined size and resolution.
• Writing pipelines with AI assistants: grounding LLMs (Claude, ChatGPT, local models) in the real API, and verifying what they produce.

Reference

• The MRMhubExperiment data object: the tables, identifiers, and feature variables of the central object.
• Function map: every function grouped by pipeline stage, linked to its reference.
• Glossary: definitions of the analytical terms used throughout the documentation.
• Design decisions: why the package is built the way it is.
• Sample types & QC roles: every sample-type (qc_type) label and its role in QC.
• Troubleshooting & FAQ: frequent problems and how to resolve them.

See also

• Tutorials: worked, end-to-end examples
• Function reference: full arguments for every function
• INTEGRATOR documentation: upstream peak integration