OTU_stats: OTU statistics

In AlmaasLab/micInt: Find microbial interactions

OTU statistics

Description

This function returns a summary of OTU statistics for the OTUs of an OTU table

Usage

OTU_stats(refined_table, taxonomy = NULL)

Arguments

refined_table	The refined OTU table returned from refine_data or a phyloseq (experiment level or otu_table) object.
taxonomy	Named character, with the names being those of the OTUs and the values their taxonomy collapased into a single string (for each OTU)

Value

A data.frame with one row for each OTU with the following elements:

• ID The OTU name

• meanAbundance

• medianAbundance

• maxAbundance

• numberNonZero The number of samples where the OTU has a non-zero abundance

• taxonomy collapsed into a single string, may be missing

#' @examples library(micInt) data("seawater") OTU_stats(seawater)

AlmaasLab/micInt documentation built on April 1, 2022, 10:37 a.m.