logLin: prepares OTU counts data for PCA analysis using...
In MCMC.OTU: Bayesian Analysis of Multivariate Counts Data in DNA Metabarcoding and Ecology
Description
Usage
Arguments
Value
Author(s)
References
Description
Normalizes counts based on total counts per sample, then uses log-linear-hybrid
transformation on the data.
Usage
1
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/
MCMC.OTU documentation built on May 1, 2019, 10:55 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) References
Description
Normalizes counts based on total counts per sample, then uses log-linear-hybrid transformation on the data.
Usage
1 |
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/
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.