import_sintax_file: Import sintax Taxonomy File

In jfq3/RDPutils: R Utilities for Processing RDPTool Output

Description

Converts the tab-delimited output of USEARCH's (version 9+) sintax command to a phyloseq tax_table object. The confidence level for taxonomic assignment is chosen on import.

Usage

import_sintax_file(in_file, confidence = 0.8)

Arguments

in_file	A sintax file.
confidence	The confidence level to use in assigning taxonomic categories

Details

The sintax algorithm is new to USEARCH 9. It does not require training and still calculates the confidence with which taxonomic assignments are made. It does this by a method purported to be more accurate than the RDP classifier method. This function allows choice of the confidence level (0.8 by default) at the time the file is imported as a phyloseq tax_table.

Value

A phyloseq tax_table.

Author(s)

John Quensen

References

Edgar, R.C. (2016), SINTAX, a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, http://dx.doi.org/10.1101/074161.

Examples

##---- Not run. ----
##-- import_sintax_file(in_file="sintax_result.txt", confidence = 0.8)

jfq3/RDPutils documentation built on Nov. 8, 2019, 1:05 p.m.