css_pq: Cumulative Sum Scaling (CSS) normalization of a phyloseq...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Cumulative Sum Scaling (CSS) normalization of a phyloseq object

Description

Wrapper around metagenomeSeq::cumNorm() / metagenomeSeq::MRcounts() implementing Cumulative Sum Scaling (Paulson et al. 2013, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nmeth.2658")}).

Usage

css_pq(physeq, log = TRUE)

Arguments

physeq	(required) a phyloseq-class object obtained using the phyloseq package.
log	(logical, default TRUE) whether to return \log_2(x + 1) transformed counts (as recommended by the metagenomeSeq authors).

Value

A new phyloseq-class object with a CSS normalised otu_table.

Author(s)

Adrien Taudière

See Also

metagenomeSeq::cumNorm()

Examples

data_f_css <- css_pq(data_fungi_mini)

MiscMetabar documentation built on June 8, 2026, 5:07 p.m.