bootstrap.microbes: bootstrap.microbes

In microbiome/microbiomeold: Tools for microbiome analysis

Description

Bootstrap method for core microbiota estimation from Salonen et al. (2012)

Usage

bootstrap.microbes(D, Nsample = NULL, minPrev = 2, Nboot = 1000,
  I.thr = 1.8, ncore = 1, I.max = NULL)

Arguments

D	data (phylotypes x samples)
Nsample	bootstrap sample size, default is the same size as data
minPrev	Lower limit for number of samples where microbe needs to exceed the intensity threshold for a 'present' call.
Nboot	bootstrap sample size
I.thr	Lower limit for intensity threshold
ncore	number of nodes for parallelization - default 1
I.max	Upper limit for intensity threshold. Later addition. set to NULL (default) to replicate Salonen et al.

Value

data frame with microbes and their frequency of presence in the core

Author(s)

Contact: Jarkko Salojarvi [e-mail]

References

The core microbiota bootstrap method implemented with this function: Salonen A, Salojarvi J, Lahti L, de Vos WM. The adult intestinal core microbiota is determined by analysis depth and health status. Clinical Microbiology and Infection 18(S4):16-20, 2012

To cite this R package, see citation("microbiome")

Examples

data(peerj32);
	     bs <- bootstrap.microbes(t(peerj32$microbes), Nboot = 5)

microbiome/microbiomeold documentation built on May 22, 2019, 9:57 p.m.