import_rdp_tax_table: Import RDP Classifier Taxonomy Table

In speedytax: Rapidly Import Classifier Results into 'phyloseq'

Import RDP Classifier Taxonomy Table

Description

Imports fixed rank taxonomy files created with the RDP Classifier

Usage

import_rdp_tax_table(in_file, confidence)

Arguments

in_file	A fix-rank tab-delimited text file output by the RDP Classifier
confidence	The confidence level for filtering the taxonomy

Details

The RDP Classifier must be given the option -f fixrank (or –format fixrank) in order for this importer to work correctly.

A confidence value of 0.8 for is recommended for full-length 16S rRNA gene sequences and a value of 0.5 is recommended for shorter amplicons.

Value

A phyloseq tax_table object

References

Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267.

Examples

taxonomy_file <- system.file("extdata", "rdp_table.tsv", package = "speedytax")
example_tax_table <- import_rdp_tax_table(in_file = taxonomy_file)
example_tax_table

speedytax documentation built on May 29, 2024, 2:47 a.m.