Make.CLR: Make.CLR
In jbisanz/MicrobeR: Handy functions for microbiome analysis in R
Description
Usage
Arguments
Value
Description
Takes a table of Features/OTUs/SVs and converts to centered log2 ratio abundances. See:
Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data
Gregory B. Gloor, Gregor Reid; Canadian Journal of Microbiology, 2016, 62:692-703, 10.1139/cjm-2015-0821
For information on CZM replacement see : Martin-Fernandez, J.A., Hron, K., Templ, M., Filzmoser, P., Palarea-Albaladejo, J. Bayesian-multiplicative treatment of count zeros in compositional data sets. Statistical Modelling 2015; 15 (2): 134-158.
Usage
1
Make.CLR(FEATURES, PRIOR, CZM)
Arguments
FEATURES
Table of feature/OTU/SV counts where Samples are columns, and IDs are row names
PRIOR
A numeric value to add before log transformation (default 0.5). *Ignored if CZM=TRUE
CZM
Should count zero multiplicative method be used instead of adding simple prior (TRUE/FALSE, defaults to FALSE)
Value
Table of CLR-normalized Abundances (log2)
jbisanz/MicrobeR documentation built on June 5, 2019, 7:53 p.m.
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Description Usage Arguments Value
Description
Takes a table of Features/OTUs/SVs and converts to centered log2 ratio abundances. See: Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data Gregory B. Gloor, Gregor Reid; Canadian Journal of Microbiology, 2016, 62:692-703, 10.1139/cjm-2015-0821 For information on CZM replacement see : Martin-Fernandez, J.A., Hron, K., Templ, M., Filzmoser, P., Palarea-Albaladejo, J. Bayesian-multiplicative treatment of count zeros in compositional data sets. Statistical Modelling 2015; 15 (2): 134-158.
Usage
1 | Make.CLR(FEATURES, PRIOR, CZM)
|
Arguments
FEATURES |
Table of feature/OTU/SV counts where Samples are columns, and IDs are row names |
PRIOR |
A numeric value to add before log transformation (default 0.5). *Ignored if CZM=TRUE |
CZM |
Should count zero multiplicative method be used instead of adding simple prior (TRUE/FALSE, defaults to FALSE) |
Value
Table of CLR-normalized Abundances (log2)
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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