logLin

0th

Percentile

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.

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.

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/

Aliases
  • logLin
Documentation reproduced from package MCMC.OTU, version 1.0.10, License: GPL-3

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