core_members: Core Taxa

In microbiome/microbiome: Microbiome Analytics

Core Taxa

Description

Determine members of the core microbiota with given abundance and prevalences

Usage

core_members(x, detection = 1/100, prevalence = 50/100, include.lowest = FALSE)

Arguments

x	phyloseq-class object
detection	Detection threshold for absence/presence (strictly greater by default).
prevalence	Prevalence threshold (in [0, 1]). The required prevalence is strictly greater by default. To include the limit, set include.lowest to TRUE.
include.lowest	Include the lower boundary of the detection and prevalence cutoffs. FALSE by default.

Details

For phyloseq object, lists taxa that are more prevalent with the given detection threshold. For matrix, lists columns that satisfy these criteria.

Value

Vector of core members

Author(s)

Contact: Leo Lahti [e-mail]

References

A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')

Examples

data(dietswap)
# Detection threshold 1 (strictly greater by default);
# Note that the data (dietswap) is here in absolute counts
# (and not compositional, relative abundances)
# Prevalence threshold 50 percent (strictly greater by default)
a <- core_members(dietswap, 1, 50/100)

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