Find the Top Taxa — findTopTaxa • biomeUtils

Find the Top Taxa

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

References

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

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
findTopTaxa(FuentesIliGutData, top= 5L, method="prevalence")
#> [1] "ASV1"  "ASV22" "ASV4"  "ASV15" "ASV21"