phyloseq_transform_rlog_blind: Regularized-log (rlog) transformation of OTU abundance table.

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Regularized-log (rlog) transformation of OTU abundance table.

Description

Regularized-log (rlog) transformation of OTU abundance table.

Usage

phyloseq_transform_rlog_blind(physeq, dropneg = F, dropmissing = T, ...)

Arguments

physeq	A phyloseq-class object
dropneg	Logical, replace negative transformed values with 0
dropmissing	Logical, remove missing data
...	Additional arguments will be passed to rlogTransformation

Details

rlog transformation (this function) is preferable to the vst (phyloseq_transform_vst_blind) if the size factors vary widely.

Value

Phyloseq object with transformed counts in OTU table.

See Also

phyloseq_transform_vst_blind, phyloseq_transform_css, rlog, varianceStabilizingTransformation

vmikk/metagMisc documentation built on Feb. 14, 2024, 2:29 a.m.