vst_pq: Variance Stabilizing Transformation of a phyloseq object...

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Variance Stabilizing Transformation of a phyloseq object (DESeq2)

Description

Wrapper around DESeq2::varianceStabilizingTransformation() (Love, Huber & Anders 2014, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s13059-014-0550-8")}). Counts are incremented by 1 to handle zeros before VST is applied.

Usage

vst_pq(physeq, blind = TRUE, fitType = "parametric")

Arguments

physeq	(required) a phyloseq-class object obtained using the phyloseq package.
blind	(logical, default TRUE) passed to DESeq2.
fitType	(character, default "parametric") passed to DESeq2.

Value

A new phyloseq-class object with a VST transformed otu_table.

Author(s)

Adrien Taudière

See Also

DESeq2::varianceStabilizingTransformation()

Examples

data_f_vst <- vst_pq(data_fungi_mini)

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