Overview¶

These examples are small, runnable scripts for taking first steps in learning the public emzed API. Each example also has an executed notebook version (.ipynb) with captured output; the documentation pages are generated from those notebooks.

Download all examples (scripts, notebooks, and data files) as a single archive: examples.zip.

Start here:

• Table basics: create, filter, and reshape an emzed.Table
• I/O basics: save and load .table, CSV, and Excel files
• Chemistry basics: formulas, isotopes, adducts, and abundance helpers
• Formula from m/z: fit molecular-formula candidates to an observed mass
• PubChem lookup: query the local cached PubChem compound table
• Targeted annotation: build a candidate space and annotate adducts
• Feature finding with FeatureFinderMetabo: detect features in a small mzXML file
• Peak integration: integrate peak areas from an existing peak table
• Chromatogram integration: extract chromatograms and integrate peak areas
• Table expressions: derive columns with expressions and filter by conditions
• Table manipulations: join tables and compute grouped summaries
• Out-of-memory processing: combine peak tables from many samples without loading them into RAM
• R interpreter bridge: run R code, convert data.frames into emzed.Table

Most examples avoid XCMS/feature-finder workflows so beginners can run them without installing R first. The FeatureFinderMetabo example is the exception and notes its R/XCMS requirement explicitly.