get_taxa_nomy: Taxa/OTU abundance in a given sample coupled with rank and...

Description Usage Arguments Value See Also

View source: R/convenience_functions.R

Description

Taxa/OTU abundance in a given sample coupled with rank and taxonomic information

Usage

1
get_taxa_nomy(physeq, smp, level = "Species")

Arguments

physeq

phyloseq-class

smp

A single sample of interest. This integer or sample name will be passed to get_taxa.

level

A character indicating the taxonomic rank of interest. Should be in rank_names. Default is "Species".

Value

An abundance sorted data.frame with the following components

Sample

Sample of interest

Abundance

Taxa/OTU abundance in the sample of interest

Rank

Taxa/OTU rank in the dataset. The higher the rank, the less abundant the OTU.

level

Taxonomic rank of interest. Note that the column is named after the provided value from level.

See Also

get_taxa


cpauvert/psadd documentation built on May 13, 2019, 10:54 p.m.