logLin function

prepares OTU counts data for PCA analysis using log-linear-hybrid transform

Normalizes counts based on total counts per sample, then uses log-linear-hybrid transformation on the data.

logLin(data,count.columns,k=10,zero.na=FALSE)

Arguments

• data: OTU counts table. Rows: samples, columns: OTUs.
• count.columns: numbers of colums containing OTU counts.
• k: count threshold to transition from linear to log transform.
• zero.na: With 'zero.na=TRUE', the original zero count datapoints become 'NA' (useful for analysis of pairwise correlations between OTUs).

Returns

A table of transformed normalized values.

References

Log-linear-hybrid 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