In eclarke/metaglomr: Tools for tidy metagenomics

knitr::opts_chunk$set(echo = TRUE, collapse=TRUE)

This is a package to combine counts, sample metadata, and taxonomic annotations into one long-form tidy dataframe for further analysis. It offers functions to switch between phyloseq objects and these 'agglomerated' dataframes.

Read the documentation.

Installation

devtools::install_github("eclarke/metaglomr")

Short usage overview

suppressPackageStartupMessages(library(tidyverse))
library(metaglomr)

data(features)  # A counts matrix, with rows as samples and columns as features
data(samples)   # A dataframe with sample metadata
data(taxa)      # A dataframe or matrix with taxonomic annotations for features

# Combine all of these datasets into one long-form dataframe
(agg <- agglomerated(features, samples, taxa, "sample_id"))

eclarke/metaglomr documentation built on May 30, 2019, 12:46 p.m.