phyloseq2metagenomeSeq: Convert phyloseq data to MetagenomeSeq 'MRexperiment' object

In yiluheihei/microbiomeMarker: microbiome biomarker analysis toolkit

Convert phyloseq data to MetagenomeSeq MRexperiment object

Description

The phyloseq data is converted to the relevant metagenomeSeq::MRexperiment object, which can then be tested in the zero-inflated mixture model framework in the metagenomeSeq package.

Usage

phyloseq2metagenomeSeq(ps, ...)

otu_table2metagenomeSeq(ps, ...)

Arguments

ps	phyloseq::phyloseq object for phyloseq2metagenomeSeq(), or phyloseq::otu_table object for otu_table2metagenomeseq().
...	optional, additional named arguments passed to metagenomeSeq::newMRexperiment(). Most users will not need to pass any additional arguments here.

Value

A metagenomeSeq::MRexperiment object.

See Also

metagenomeSeq::fitTimeSeries(), metagenomeSeq::fitLogNormal(),metagenomeSeq::fitZig(), metagenomeSeq::MRtable(),metagenomeSeq::MRfulltable()

Examples

data(caporaso)
phyloseq2metagenomeSeq(caporaso)

yiluheihei/microbiomeMarker documentation built on Nov. 5, 2023, 7:19 a.m.