startedLog function

prepares OTU counts data for PCA analysis using started-log transform

Normalizes counts based on total counts per sample, adds a constant number (argument logstart) to get rid of zeroes, then log-transforms the data.

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).

Returns

A table of log-transformed normalized values.

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/

Author(s)

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