findTopTaxa: Find the Top Taxa

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

Find the Top Taxa

Description

Find the Top Taxa

Usage

findTopTaxa(x, top = 5L, method = c("mean", "sum", "median", "prevalence"))

Arguments

x	A phyloseq object
top	Numeric value, how many top taxa to return. Default return top five taxa.
method	Specify the method to determine top taxa. Either sum, mean, median or prevalence. Default is 'mean'.

Value

A vector of the most top abundant taxa

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

Examples

library(biomeUtils)
data("FuentesIliGutData")
findTopTaxa(FuentesIliGutData, top= 5L, method="prevalence")

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.