otuStack {MCMC.OTU}

Prepares OTU counts data for MCMC model fitting using mcmc.otu().

Description

Stacks all OTU columns into one (count), creates a column for OTU names and columns for experimental conditions. Adds a fake OTU called "summ" - sum of all counts per sample.

Usage

otuStack(data, count.columns, condition.columns)

Arguments

data

The input data table: one column per OTU, plus columns containg experimental conditions and the required column 'sample' denoting biological replicates. See green.data included with the package.

count.columns

vector of numbers identifyng OTU counts columns

condition.columns

vector of numbers identifyng columns containing experimental conditions

Value

A dataset that can be fed into mcmc.otu() function.

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/

Examples

# Symbiodinium sp diversity in two coral species at two reefs (banks)
data(green.data)
green.data

# stacking the data table
gs=otuStack(green.data,count.columns=c(4:8),condition.columns=c(1:3))
head(gs,30)