rare: Rare Microbiota

In microbiome: Microbiome Analytics

Description

Filter the phyloseq object to include only rare (non-core) taxa.

Usage

rare(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]; strictly greater by default)
include.lowest	Include the lower boundary of the detection and prevalence cutoffs in core calculation. FALSE by default.
...	Arguments to pass.

Value

Filtered phyloseq object including only rare 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

Examples

data(dietswap)
# Detection threshold 0 (strictly greater by default);
# Prevalence threshold 50 percent (strictly greater by default)
pseq <- rare(dietswap, 0, 50/100)

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