prevalence: OTU Prevalence

In microbiome: Microbiome Analytics

Description

Simple prevalence measure.

Usage

prevalence(
  x,
  detection = 0,
  sort = FALSE,
  count = FALSE,
  include.lowest = FALSE
)

Arguments

x	A vector, data matrix or phyloseq object
detection	Detection threshold for absence/presence (strictly greater by default).
sort	Sort the groups by prevalence
count	Logical. Indicate prevalence as fraction of samples (in percentage [0, 1]; default); or in absolute counts indicating the number of samples where the OTU is detected (strictly) above the given abundance threshold.
include.lowest	Include the lower boundary of the detection and prevalence cutoffs. FALSE by default.

Details

For vectors, calculates the fraction (count=FALSE) or number (count=TRUE) of samples that exceed the detection. For matrices, calculates this for each matrix column. For phyloseq objects, calculates this for each OTU. The relative prevalence (count=FALSE) is simply the absolute prevalence (count=TRUE) divided by the number of samples.

Value

For each OTU, the fraction of samples where a given OTU is detected. The output is readily given as a percentage.

Author(s)

Contact: Leo Lahti [e-mail]

References

A Salonen et al. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16 20, 2012. To cite the microbiome R package, see citation('microbiome')

Examples

data(peerj32)     
pr <- prevalence(peerj32$phyloseq, detection=0, sort=TRUE, count=TRUE)

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