update_assignment: Update the taxonomic assignment of a phyloseq object
In ammararuby/MButils: Utility functions for DNA metabarcoding
View source: R/update_assignment.R
update_assignment R Documentation
Update the taxonomic assignment of a phyloseq object
Description
Replaces the tax_table slot of a phyloseq object with
updated assignments based on a revised version of a reference database.
Usage
update_assignment(ps, ref, use_function = "species")
Arguments
ps
Phyloseq object to be updated
ref
Path to the reference database (a FASTA file) to use for
assignment
use_function
One of either 'species' or 'taxonomy',
indicating if reference database is use_functionted for species
(assignSpecies) or taxonomy (assignTaxonomy) assignment.
Defaults to 'species' with the MButils assignSpecies_mod
function.
Value
An updated phyloseq object.
ammararuby/MButils documentation built on Jan. 29, 2023, 11:13 a.m.
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View source: R/update_assignment.R
| update_assignment | R Documentation |
Update the taxonomic assignment of a phyloseq object
Description
Replaces the tax_table slot of a phyloseq object with
updated assignments based on a revised version of a reference database.
Usage
update_assignment(ps, ref, use_function = "species")
Arguments
ps |
Phyloseq object to be updated |
ref |
Path to the reference database (a FASTA file) to use for assignment |
use_function |
One of either |
Value
An updated 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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