core: Core Microbiota

In microbiome: Microbiome Analytics

Description

Filter the phyloseq object to include only prevalent taxa.

Usage

core(x, detection, prevalence, 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.
...	Arguments to pass.

Value

Filtered phyloseq object including only prevalent taxa

Author(s)

Contact: Leo Lahti [e-mail]

References

Salonen A, Salojarvi J, Lahti L, de Vos WM. 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')

See Also

core_members, rare_members

Examples

data(dietswap)
# Detection threshold 0 (strictly greater by default);
# Prevalence threshold 50 percent (strictly greater by default)
pseq <- core(dietswap, 0, 50/100)
# Detection threshold 0 (strictly greater by default);
# Prevalence threshold exactly 100 percent; for this set
# include.lowest=TRUE, otherwise the required prevalence is 
# strictly greater than 100
pseq <- core(dietswap, 0, 100/100, include.lowest = TRUE)

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.