phy_BasicStats: Basic Phyloseq stats

In g-antonello/gautils2: Wrapper of my functions to wrangle mostly microbiome data

Basic Phyloseq stats

Description

Generate a data frame with prevalence, mean abundance and variance of the taxa in a phyloseq object

Usage

phy_BasicStats(physeq, transform)

Arguments

physeq	Either a phyloseq or a otu.table or a matrix object. If you have a matrix, make sure taxa are on the rows
transform	Any transformation function allowed by phy_transform

Value

A data.frame object

Examples

data(GlobalPatterns)
gp_genus <- tax_glom(GlobalPatterns, "Genus")
basic_statistics <- phy_BasicStats(gp_genus, transform = "clr")

g-antonello/gautils2 documentation built on Nov. 28, 2022, 9:39 a.m.