CommonTaxa: Identify the most abundant and prevalent taxa

In katrikorpela/mare: Microbiota Analysis in R Easily

Identify the most abundant and prevalent taxa

Description

Creates a list with two components, 'Abundant' and 'Prevalent', listing the names of the most abundant and most prevalent taxa. This is the only function in the package mare that saves the output as an R object (and therefore has to be assigned a name).

Usage

CommonTaxa(taxonomic.table, mean.abundance, prevalence)

Arguments

taxonomic.table	Name of the taxonomic table. Should be a text file.
mean.abundance	Relative abundance cut-off: taxa with higher relative abundances are shown. Should be a value between 0-1.
prevalence	Prevalence cut-off: taxa occurring in a higher proportion of samples will be shown. Should be a value between 0-1.

Value

A list of the most abundant and prevalent taxa.

Abundant	The most abundant taxa in the samples.
Prevalent	The most prevalent taxa in the samples.

Author(s)

Katri Korpela

Examples

## Not run: 
#Identify the genus-level taxa whose mean relative abundance is >5 percent and those that 
#occur in >50 percent of all samples.
common <- CommonTaxa(taxonomic.table = 'organised_genus_table.txt',
                     mean.abundance = 0.05,
                     prevalence = 0.5)
abundant <- unlist(common[1])
prevalent <- unlist(common[2])

## End(Not run)

katrikorpela/mare documentation built on July 17, 2022, 2:49 a.m.