startedLog: prepares OTU counts data for PCA analysis using started-log...
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, adds a constant number
(argument logstart) to get rid of zeroes, then log-transforms the data.
Usage
1
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).
Value
A table of log-transformed normalized values.
Author(s)
Mikhail V. Matz, University of Texas at Austin
<matz@utexas.edu>
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/
MCMC.OTU documentation built on May 1, 2019, 10:55 p.m.
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Description Usage Arguments Value Author(s) References
Description
Normalizes counts based on total counts per sample, adds a constant number (argument logstart) to get rid of zeroes, then log-transforms the data.
Usage
1 | 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). |
Value
A table of log-transformed normalized values.
Author(s)
Mikhail V. Matz, University of Texas at Austin <matz@utexas.edu>
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/
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.
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