phyloseq_transform_css: Cumulative sum scaling (CSS) normalization of OTU abundance...

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Cumulative sum scaling (CSS) normalization of OTU abundance table.

Description

Cumulative sum scaling (CSS) normalization of OTU abundance table.

Usage

phyloseq_transform_css(physeq, norm = TRUE, log = TRUE, ...)

Arguments

physeq	A phyloseq-class object
norm	Logical, return normalized counts
log	Logical, apply a logarithmic transform (log2) to the normalized count data
...	Additional arguments will be passed to MRcounts

Details

Median scaling factor across samples will be used as default.

Value

Phyloseq object with transformed counts in OTU table.

References

Paulson et al. Nature Methods 10, 1200–1202 (2013) doi:10.1038/nmeth.2658. http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html

See Also

phyloseq_transform_vst_blind, phyloseq_transform_rlog_blind, rlog, varianceStabilizingTransformation

Examples

data("GlobalPatterns")
gp_tr <- phyloseq_transform_css(GlobalPatterns)
head(otu_table(gp_tr))

# Ordination on CSS-transformed data
plot_ordination(physeq = gp_tr, ordination = ordinate(gp_tr, method = "PCoA", distance = "bray"), color = "SampleType")
# Ordination on raw data
plot_ordination(physeq = GlobalPatterns, ordination = ordinate(GlobalPatterns, method = "PCoA", distance = "bray"), color = "SampleType")

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.