Cumulative Sum Scaling (CSS) normalization of a phyloseq object

Wrapper around metagenomeSeq::cumNorm() / metagenomeSeq::MRcounts() implementing Cumulative Sum Scaling (Paulson et al. 2013, 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.

See also

metagenomeSeq::cumNorm()

Author

Adrien Taudière

Examples

data_f_css <- css_pq(data_fungi_mini)
#> Warning: cumNormStatFast() failed (likely samples with <=1 feature); falling back to cumNormStat(). Original error: Warning sample with one or zero features
#> Default value being used.