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Conduit Object
The Conduit object is the final output of the Snakemake workflow. It is an R S4 object generated by the conduitR package and contains all key information from a metaproteomics experiment in a single portable file.
It can be loaded into R:
conduit <- readRDS("experiments/my_experiment/runs/my_run/output_files/my_experiment_my_run_conduit.rds")and used with the tools provided by conduitR, or opened directly in Conduit-GUI for interactive exploration without writing code.
The Conduit object is a custom S4 object with the following slots:
1. Database The protein database used to generate the search space. Contains information about proteomes, peptide sequences, and how the database was constructed.
2. QC Metrics Quality control metrics for the experiment.
3. Taxonomy A lookup table linking NCBI taxon IDs, UniProt proteomes, and other taxonomic metadata.
4. Annotation A functional annotation lookup table providing GO terms, KEGG pathways, Pfam domains, CAZy, and eggNOG annotations for proteins in the database.
5. QFeatures A QFeatures object that holds:
-
colData: sample metadata (experimental conditions, replicates) -
rowData: observation-specific information (peptide- or protein-level measurements) - Quantitative data from DIA-NN, ready for downstream statistical analysis
- All relevant experimental information — metadata, quantitative measurements, taxonomy, and annotations — is stored in a single, portable object.
- The object is designed to be extendable; future versions of conduitR can add new slots without breaking compatibility.
- The hierarchical structure (precursor → peptide → protein → taxonomy) is fully navigable via conduitR's accessor functions.