format_phyloseq {microbiomeutilities}R Documentation

Formatting the phyloseq-class Object

Description

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

Usage

format_phyloseq(x)

Arguments

x

phyloseq-class object

Details

Most commonly it is observed that the taxonomy file has classification until a given taxonomic level. Hence, to avoid loss of OTU information while using the function tax_glom() for merging at a specific taxonomic level. we will fill the empty cells with the maximum classification available along with the OTU number. 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: 
library(microbiome)
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
p0.f <- format_phyloseq(p0)
head(tax_table(p0.f))

## End(Not run)


[Package microbiomeutilities version 0.99.02 Index]