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Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
23 lines
1.2 KiB
Markdown
23 lines
1.2 KiB
Markdown
# Taxonomic Analysis Functions in `obiseq` Package
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This module provides tools for assigning taxonomic labels to biological sequences using a reference taxonomy.
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- **`TaxonomicDistribution(taxonomy)`**:
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Returns a map from taxonomic nodes to read counts, based on `taxid` annotations in the sequence metadata. It validates taxids against the taxonomy and enforces strict handling of aliases.
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- **`LCA(taxonomy, threshold)`**:
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Computes the *Lowest Common Ancestor* (LCA) of all taxonomic assignments for a sequence, weighted by their abundances.
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- Iteratively traverses upward from each taxon’s path in the taxonomy tree.
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- At each level, computes the relative weight (`rmax`) of the most frequent taxon.
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- Stops when `rmax < threshold`, returning:
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• the LCA taxon,
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• its confidence score (`rans`), and
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• total read count used.
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- **`AddLCAWorker(...)`**:
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Creates a `SeqWorker` function to annotate sequences with LCA results:
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- Sets attributes like `<slot>_taxid`, `<slot>_name`, and `<slot>_error` (rounded to 3 decimals).
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- Automatically appends `_taxid` if missing in `slot_name`.
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All functions integrate with the OBITools4 ecosystem, supporting robust taxonomic inference for metabarcoding workflows.
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