core_matrix: Core Matrix

In microbiome/microbiome: Microbiome Analytics

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 [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

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

microbiome/microbiome documentation built on Dec. 12, 2024, 2:45 p.m.