core_matrix {microbiome}R Documentation

Core Matrix

Description

Creates the core matrix.

Usage

core_matrix(x, prevalences = seq(0.1, 1, , 1), detections = NULL)

Arguments

x

phyloseq object or a taxa x samples abundance matrix

prevalences

a vector of prevalence percentages in [0,1]

detections

a vector of intensities around the data range

Value

Estimated core microbiota

Author(s)

Contact: Jarkko Salojarvi microbiome-admin@googlegroups.com

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

## Not run: 
    # Not exported
    data(peerj32)
    core <- core_matrix(peerj32$phyloseq)

## End(Not run)

[Package microbiome version 1.4.2 Index]