agglomerated: Create an agglomerated dataframe.

In eclarke/metaglomr: Tools for tidy metagenomics

Description

Creates an agglomerated dataframe from feature counts, sample metadata, and taxonomy annotations.

Usage

agglomerated(features, samples, taxonomy, sample_col, otu_col = "otu_id",
  count_col = "count")

Arguments

features	a matrix-like object with features as columns and samples as rows
samples	an optional dataframe containing sample metadata, with each sample a separate row
taxonomy	an optional dataframe containing taxonomy information, with each taxa a row and rownames providing taxa id
sample_col	a string giving the name of the column in 'samples' corresponding to the rows in the features table
otu_col	a string giving the desired name of the otu column in the resulting dataframe
count_col	a string giving the desired name of the counts column in the resulting dataframe

Value

A dataframe with each row representing a unique feature+sample+count observation, plus any metadata about the sample and any taxonomic annotation about the feature. This results in a lot of repetition, but is very easy to manipulate with dplyr and the tidyverse.

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