srs_pq: Scaling with Ranked Subsampling (SRS) normalization of a...
In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis
srs_pq R Documentation
Scaling with Ranked Subsampling (SRS) normalization of a phyloseq object
Description
Wrapper around SRS::SRS() (Heidrich et al. 2021,
\Sexpr[results=rd]{tools:::Rd_expr_doi("10.7717/peerj.9593")}) which scales all samples to a common count
Cmin while preserving the rank order of OTU abundances.
Usage
srs_pq(physeq, Cmin = NULL, ...)
Arguments
physeq
(required) a phyloseq-class object obtained
using the phyloseq package.
Cmin
(integer) the common scaling depth. Defaults to
min(sample_sums(physeq)).
...
Additional arguments passed on to SRS::SRS().
Value
A new phyloseq-class object with the SRS
normalised otu_table.
Author(s)
Adrien Taudière
See Also
SRS::SRS(), rarefy_pq()
Examples
data_f_srs <- srs_pq(data_fungi_mini)
sample_sums(data_f_srs)
MiscMetabar documentation built on June 8, 2026, 5:07 p.m.
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| srs_pq | R Documentation |
Scaling with Ranked Subsampling (SRS) normalization of a phyloseq object
Description
Wrapper around SRS::SRS() (Heidrich et al. 2021,
\Sexpr[results=rd]{tools:::Rd_expr_doi("10.7717/peerj.9593")}) which scales all samples to a common count
Cmin while preserving the rank order of OTU abundances.
Usage
srs_pq(physeq, Cmin = NULL, ...)
Arguments
physeq |
(required) a |
Cmin |
(integer) the common scaling depth. Defaults to
|
... |
Additional arguments passed on to |
Value
A new phyloseq-class object with the SRS
normalised otu_table.
Author(s)
Adrien Taudière
See Also
SRS::SRS(), rarefy_pq()
Examples
data_f_srs <- srs_pq(data_fungi_mini)
sample_sums(data_f_srs)
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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