In tbradley1013/KEGGerator: Identify genomic functionality with KEGG

knitr::opts_chunk$set(
  collapse = TRUE,
  echo = TRUE,
  warning = FALSE,
  message = FALSE,
  comment = "#>"
)

This goal of this vignette is to walk you through the basic functionality of the KEGGerator package. This package is designed for use with data gerenated using the dada2 package, in the form of a phyloseq object. For this walk-through, we will use the GlobalPatterns dataset from the phyloseq package.

library(phyloseq)
library(KEGGerator)
library(tidyverse)

patterns_file <- system.file("data", "GlobalPatterns.Rdata", package = "phyloseq")
load(patterns_file)

# Filter data for runtime effeciency - reduces dataset to ~10% of original size
patterns <- filter_taxa(GlobalPatterns, function(x)sum(x)>10000, prune = TRUE)

patterns_tax <- tax_tibble(patterns)
patterns_genomes <- genomes_tibble(patterns)

First,

tbradley1013/KEGGerator documentation built on Feb. 23, 2020, 6:44 a.m.