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]). 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.

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 1.8.0 Index]