lca: Find the last common ancestor of assignSpecies taxonomic...
In ammararuby/MButils: Utility functions for DNA metabarcoding
lca R Documentation
Find the last common ancestor of assignSpecies taxonomic assignments
Description
The output of the assignSpecies_mod function is a
two-column dataframe of ASVs and their taxonomic assignments based on exact
matching to reference sequences: if multiple sequences are matched, the ASV
will be repeated across rows, one per match. This function collapses each
ASV to a single row labeled with the last common ancestor of all its
matched taxa (*e.g.*, an ASV matching to an ASV matching to both wheat
[Triticum aestivum] and rye [Secale cereale] was relabeled as Poaceae, the
family shared by both genera).
Usage
lca(assignment)
Arguments
assignment
The output of assignSpecies_mod (*i.e.* matches of
ASVs to sequences in a metabarcoding reference database).
Value
A taxonomy table with taxonomic assignment per ASV, compatible for
use in a phyloseq object.
ammararuby/MButils documentation built on Jan. 29, 2023, 11:13 a.m.
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| lca | R Documentation |
Find the last common ancestor of assignSpecies taxonomic assignments
Description
The output of the assignSpecies_mod function is a
two-column dataframe of ASVs and their taxonomic assignments based on exact
matching to reference sequences: if multiple sequences are matched, the ASV
will be repeated across rows, one per match. This function collapses each
ASV to a single row labeled with the last common ancestor of all its
matched taxa (*e.g.*, an ASV matching to an ASV matching to both wheat
[Triticum aestivum] and rye [Secale cereale] was relabeled as Poaceae, the
family shared by both genera).
Usage
lca(assignment)
Arguments
assignment |
The output of |
Value
A taxonomy table with taxonomic assignment per ASV, compatible for use in a phyloseq object.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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