rare_members: Rare Taxa

In microbiome/microbiome: Microbiome Analytics

Rare Taxa

Description

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

Usage

rare_members(x, detection = 1/100, prevalence = 50/100, 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.

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 abundaneces accepted). For matrix, lists columns that satisfy these criteria.

Value

Vector of rare taxa

Author(s)

Leo Lahti [e-mail]

References

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

See Also

core_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)

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.