prevalence: Prevalence of features (OTUs/ASVs)

In antonioggsousa/micrUBIfuns: Set of functions for microbiome analyses

Description

Given a phyloseq object and a taxonomic rank (character) it gives the prevalence of features (OTUs/ASVs), i.e., the number of samples where each feature (OTUs/ASVs) appear (observed) grouped by taxonomic rank.

Usage

prevalence(physeq, tax_rank)

Arguments

physeq	phyloseq-class object.
tax_rank	taxonomic rank (character). One of the taxonomic ranks among the column names of 'tax_table()' of the 'physeq' object given.

Value

A data frame with Feature_ID (lists the unique features (OTUs/ASVs)), "Feature_[tax_rank]" (lists the taxonomic affiliation at the taxonomic rank defined by 'tax_rank', Feature_Abundance (absolute abundance of each feature), Feature_Relative (relative abundance of each feature), Prevalence (prevalence of each feature - the no. of samples where each feature is observed), Prevalence_Relative (the same as Prevalence, but in relative abundance).

antonioggsousa/micrUBIfuns documentation built on Nov. 14, 2020, 1:40 a.m.