noncore_members {microbiome} | R Documentation

## Select Non-Core Taxa

### Description

Filter the phyloseq object to include only taxa that do not belong to the core set defined by the detection and prevalence thresholds.

### Usage

    noncore_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]). 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.

### Value

Filtered phyloseq object including only rare taxa

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

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

### Examples

    #data(peerj32)
    #pseq <- noncore_members(peerj32$phyloseq, 200, 20/100)

[Package microbiome version 1.8.0 Index]