add_besthit: Adds 'best_hist' to a 'phyloseq-class' Object

In microbiome/microbiome: Microbiome Analytics

Adds best_hist to a phyloseq-class Object

Description

Add the lowest classification for an OTU or ASV.

Usage

add_besthit(x, sep = ":")

Arguments

x	phyloseq-class object
sep	separator e.g. ASV161:Roseburia

Details

Most commonly it is observed that taxa names are either OTU ids or ASV ids. In such cases it is useful to know the taxonomic identity. For this purpose, best_hist identifies the best available taxonomic identity and adds it to the OTU ids or ASV ids. If genus and species columns are present in input the function internally combines the names.

Value

phyloseq-class object phyloseq-class

Author(s)

Contact: Sudarshan A. Shetty [e-mail]

Examples

## Not run: 
# Example data
library(microbiome)
data(dietswap)
p0.f <- add_besthit(atlas1006, sep=":")

## End(Not run)

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.