format_to_besthit {microbiomeutilities}R Documentation

Formatting the phyloseq-class Object advanced

Description

Format the phyloseq object to add the best taxonomy in phyloseq object (tax_table and otu_table).

Usage

format_to_besthit(x)

Arguments

x

phyloseq-class object

Details

Most commonly it is observed that the taxonomy file has classification until a given taxonomic level. row.names for both tax_table and otu_table have best hit, until maximun genus level (species classification with short amplicons is a myth)is made available. This code is a slight modification of the code from ampvis phyloseq-class. Here, we directly take the phyloseq object as input and make the necessary formatting.

Value

phyloseq-class object.

Examples

## Not run: 
# Example data
library(microbiome)
library(microbiomeUtilities)
library(tibble)
data("zackular2014")
p0 <- zackular2014
p0.f <- format_to_besthit(p0)

## End(Not run)

[Package microbiomeutilities version 0.99.02 Index]