getNormalizedOTUdata function

Extracts mcmc.otu model predictions

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

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

Returns

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.

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/

Author(s)

Mikhail V. Matz, University of Texas at Austin matz@utexas.edu