aggregate_rare: Aggregate Rare Groups

In microbiome: Microbiome Analytics

Description

Combining rare taxa.

Usage

aggregate_rare(x, level, detection, prevalence, include.lowest = FALSE, ...)

Arguments

x	phyloseq-class object
level	Summarization level (from rank_names(pseq))
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.
...	Arguments to pass.

Value

phyloseq-class object

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

data(dietswap)
s <- aggregate_rare(dietswap, level = 'Phylum',
    detection = 0.1/100, prevalence = 5/100)

microbiome documentation built on Nov. 8, 2020, 5:08 p.m.