phyloseq_to_metagenomeSeq: Convert phyloseq data to MetagenomeSeq MRexperiment object

In phyloseq: Handling and analysis of high-throughput microbiome census data

Description

No testing is performed by this function. The phyloseq data is converted to the relevant MRexperiment-class object, which can then be tested in the zero-inflated mixture model framework (e.g. fitZig) in the metagenomeSeq package. See the phyloseq-extensions tutorials for more details.

Usage

phyloseq_to_metagenomeSeq(physeq, ...)

Arguments

physeq	(Required). phyloseq-class.
...	(Optional). Additional named arguments passed to newMRexperiment. Most users will not need to pass any additional arguments here.

Value

A MRexperiment-class object.

See Also

fitTimeSeries fitLogNormal fitZig MRtable MRfulltable

Examples

 # Check out the vignette metagenomeSeq for more details.
 # vignette("metagenomeSeq")
 data(soilrep)
 phyloseq_to_metagenomeSeq(soilrep)

Example output

Loading required namespace: metagenomeSeq
Failed with error:  'there is no package called 'metagenomeSeq''

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.