getNormalizedOTUdata: Extracts mcmc.otu model predictions

In MCMC.OTU: Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology

Description

Generates a table of model-derived log2-transformed OTU abundances without sample effects (i.e., corresponding to predicted normalized data)

Usage

getNormalizedOTUdata(model, data, log.base=10)

Arguments

model	mcmc.otu model: the output of mcmc.otu function fitted with pr=TRUE option
data	The dataset that was analysed to generate the model (output of otuStack function)
log.base	base of the logarithm to use

Value

The function returns a list of two data frames. The first one, normData, is the model-predicted log2-transformed OTU abundances table. It has one column per OTU and one row per sample. The second data frame, conditions, is a table of experimental conditions corresponding to the normData table.

Author(s)

Mikhail V. Matz, University of Texas at Austin <[e-mail]>

References

Elizabeth A. Green, Sarah W. Davies, Mikhail V. Matz, Monica Medina Next-generation sequencing reveals cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ 2014 https://peerj.com/preprints/246/

MCMC.OTU documentation built on May 1, 2019, 10:55 p.m.