| logLin {MCMC.OTU} | R Documentation |
prepares OTU counts data for PCA analysis using log-linear-hybrid transform
Description
Normalizes counts based on total counts per sample, then uses log-linear-hybrid transformation on the data.
Usage
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). |
Value
A table of transformed normalized values.
Author(s)
Mikhail V. Matz, University of Texas at Austin <matz@utexas.edu>
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/