variable_members {microbiome}R Documentation

Variable Microbiota

Description

Filter the phyloseq object to include only variable taxa.

Usage

variable_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.

Details

Variable taxa are members of the microbiota that are not rare, and not members of the core microbiota. Such taxa reach notable abundance in a notable fraction of the population. The variable members are calculated by using the indicated prevalence threshold to define rare taxa; and its complement 1-prevalence to define core taxa. The remaining taxa are considered variable. The same detection threshold is used in all cases.

Value

Filtered phyloseq object including only variable taxa.

Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

References

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

See Also

core_members, core, rare

Examples

data(dietswap)
# Detection threshold 0 (strictly greater by default);
# Prevalence threshold 50 percent (strictly greater by default)
pseq.rel <- transform(dietswap, 'compositional')
pseq <- variable_members(pseq.rel, 0.5/100, 20/100)

[Package microbiome version 1.2.1 Index]