noncore_members {microbiome}R Documentation

Select Non-Core Taxa

Description

Filter the phyloseq object to include only taxa that do not belong to the core set defined by the detection and prevalence thresholds.

Usage

noncore_members(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. FALSE by default.

Value

Filtered phyloseq object including only rare taxa

Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

References

To cite the microbiome R package, see citation('microbiome')

Examples

data(peerj32)
pseq <- noncore_members(peerj32$phyloseq, 200, 20/100)

[Package microbiome version 1.2.1 Index]