signifOTU

<p>The output of OTUsummary function.</p>

otu.summary

p.cutoff

<p>Trawls otuWise summary tables in the data returned by OTUsummary
and returns the names of OTUs that have p-values better than 
the specified cutoff.</p>

Poisson-lognormal generalized linear mixed model analysis of multivariate counts data using MCMC, aiming to infer the changes in relative proportions of individual variables. The package was originally designed for sequence-based analysis of microbial communities ("metabarcoding", variables = operational taxonomic units, OTUs), but can be used for other types of multivariate counts, such as in ecological applications (variables = species). The results are summarized and plotted using 'ggplot2' functions. Includes functions to remove sample and variable outliers and reformat counts into normalized log-transformed values for correlation and principal component/coordinate analysis. Walkthrough and examples: http://www.bio.utexas.edu/research/matz_lab/matzlab/Methods_files/walkthroughExample_mcmcOTU_R.txt.

signifOTU: Finds differentially represented OTUs.

Description

Usage

Arguments

Value

References