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.
devtools::install_github("eclarke/metaglomr")
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"))
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