rare_members {microbiome}R Documentation

Rare Taxa

Description

Determine members of the rare microbiota with given abundance and prevalence threshold.

Usage

rare_members(x, detection = Inf, prevalence = 20/100)

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)

Details

For phyloseq object, lists taxa that are less prevalent than the given prevalence threshold. Optionally, never exceeds the given abundance threshold (by default, all abundanecs accepted). For matrix, lists columns that satisfy these criteria.

Value

Vector of rare taxa

Author(s)

Leo Lahti microbiome-admin@googlegroups.com

References

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

See Also

core_members, noncore_members

Examples

data(dietswap)
# Detection threshold: the taxa never exceed the given detection threshold
# Prevalence threshold 20 percent (strictly greater by default)
a <- rare_members(dietswap, detection=100/100, prevalence=20/100)

[Package microbiome version 1.0.2 Index]