| startedLog {MCMC.OTU} | R Documentation |
prepares OTU counts data for PCA analysis using started-log transform
Description
Normalizes counts based on total counts per sample, adds a constant number (argument logstart) to get rid of zeroes, then log-transforms the data.
Usage
startedLog(data,count.columns,logstart=0.1)
Arguments
data |
OTU counts table. Rows: samples, columns: OTUs. |
count.columns |
numbers of colums containing OTU counts. |
logstart |
number to add to zero counts before log transform. With 'logstart=0', the zero count datapoints become 'NA' (useful for analysis of pairwise correlations between OTUs). |
Value
A table of log-transformed normalized values.
Author(s)
Mikhail V. Matz, University of Texas at Austin <matz@utexas.edu>
References
Started Log transform: Rocke DM and Durbin B Bioinformatics 2003 19:966-972 (DOI: 10.1093/bioinformatics/btg107) MCMC.OTU: 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/