phyloseq_transform_aldex_clr: ALDEx2-based centred log-ratio transformation of OTU table

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

ALDEx2-based centred log-ratio transformation of OTU table

Description

ALDEx2-based centred log-ratio transformation of OTU table

Usage

phyloseq_transform_aldex_clr(physeq, variable = NULL, iter = 1)

Arguments

physeq	A phyloseq-class object
variable	Variable name (from sample_data) containing a descriptor for the samples, allowing them to be grouped and compared
iter	Number of Monte Carlo samples to use

Details

ALDEx2 generates Monte Carlo samples of the Dirichlet distribution for each sample and converts each instance using the centred log-ratio transformation.

Value

Phyloseq object with CLR-transformed OTU counts (or a list of rarefied phyloseq-objects if iter > 1).

References

Fernandes DA, Reid J, Macklaim MJ, McMurrough TA, Edgell DR, Gloor BG (2014) Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis // Microbiome 2:15. DOI: 10.1186/2049-2618-2-15

See Also

aldex.clr

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