phyloseq_ntaxa_by_tax: Count number of OTUs by taxonomic rank for each sample.

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Count number of OTUs by taxonomic rank for each sample.

Description

Count number of OTUs by taxonomic rank for each sample.

Usage

phyloseq_ntaxa_by_tax(
  physeq,
  TaxRank = "Phylum",
  relative = F,
  add_meta_data = T
)

Arguments

physeq	A phyloseq-class object
TaxRank	Name of the taxonomic rank
relative	Logical, return relative number of OTUs
add_meta_data	Logical, add sample metadata to the resulting table

Details

This function will split phyloseq object by the specified taxonomic rank

Value

Data frame with OTU counts (columns: Sample, TaxRank, N.OTU + optional sample metadata).

Examples

data(GlobalPatterns)
phylum_counts <- phyloseq_ntaxa_by_tax(GlobalPatterns, TaxRank = "Phylum")
head(phylum_counts)

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