comp_prepare_phyloseq: Prepare Phyloseq
In jfq3/QsRutils: R Functions Useful for Community Ecology

Description Usage Arguments Details Value

Prepares a phyloseq object for making comparisons of relative abundances among treatments.

1	comp_prepare_phyloseq(expt, taxrank = "Phylum", pc.filter = 0.01)

`expt`	Experiment level phyloseq object.
`taxrank`	Taxonomic rank for which to make comparisons.
`pc.filter`	Minimum percentage of total counts to include rank in result.

The otu_table in one of the returned objects has been transformed to percentages based on the original phyloseq object supplied. The taxa in both have been filtered to include only OTUs initially present at >= pc.filter times the original total counts. For both only taxrank is included in the tax_table.

A list of two modified experiemnt level phyloseq objects

jfq3/QsRutils documentation built on Jan. 18, 2021, 12:40 a.m.