tmm_pq: Trimmed Mean of M-values (TMM) normalization of a phyloseq...
In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis
tmm_pq R Documentation
Trimmed Mean of M-values (TMM) normalization of a phyloseq object
Description
Wrapper around edgeR::calcNormFactors() with method = "TMM"
(Robinson & Oshlack 2010, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/gb-2010-11-3-r25")}). Returns
counts-per-million scaled by the TMM-derived library sizes.
Usage
tmm_pq(physeq, log = FALSE)
Arguments
physeq
(required) a phyloseq-class object obtained
using the phyloseq package.
log
(logical, default FALSE) if TRUE, returns log2(cpm + 1).
Value
A new phyloseq-class object with a TMM
normalised otu_table.
Author(s)
Adrien Taudière
See Also
edgeR::calcNormFactors(), edgeR::cpm()
Examples
data_f_tmm <- tmm_pq(data_fungi_mini)
MiscMetabar documentation built on June 8, 2026, 5:07 p.m.
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| tmm_pq | R Documentation |
Trimmed Mean of M-values (TMM) normalization of a phyloseq object
Description
Wrapper around edgeR::calcNormFactors() with method = "TMM"
(Robinson & Oshlack 2010, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/gb-2010-11-3-r25")}). Returns
counts-per-million scaled by the TMM-derived library sizes.
Usage
tmm_pq(physeq, log = FALSE)
Arguments
physeq |
(required) a |
log |
(logical, default |
Value
A new phyloseq-class object with a TMM
normalised otu_table.
Author(s)
Adrien Taudière
See Also
edgeR::calcNormFactors(), edgeR::cpm()
Examples
data_f_tmm <- tmm_pq(data_fungi_mini)
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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