speedytax (version 1.0.4)

import_rdp_tax_table: Import RDP Classifier Taxonomy Table

Description

Imports fixed rank taxonomy files created with the RDP Classifier

Usage

import_rdp_tax_table(in_file, confidence)

Value

A phyloseq tax_table object

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.

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