Introduction

This code is available at https://github.com/aaronsk7/guppy-methylation

This script performs enrichment analysis of methylkit results.

Load in packages

library("R.utils")
## Loading required package: R.oo
## Loading required package: R.methodsS3
## R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
## R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.
## 
## Attaching package: 'R.oo'
## The following object is masked from 'package:R.methodsS3':
## 
##     throw
## The following objects are masked from 'package:methods':
## 
##     getClasses, getMethods
## The following objects are masked from 'package:base':
## 
##     attach, detach, load, save
## R.utils v2.10.1 (2020-08-26 22:50:31 UTC) successfully loaded. See ?R.utils for help.
## 
## Attaching package: 'R.utils'
## The following object is masked from 'package:utils':
## 
##     timestamp
## The following objects are masked from 'package:base':
## 
##     cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
##     warnings
library("parallel")
library("reshape2")
library("kableExtra")
library("dplyr")
## 
## Attaching package: 'dplyr'
## The following object is masked from 'package:kableExtra':
## 
##     group_rows
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library("RColorBrewer")
library("GenomicRanges")
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:dplyr':
## 
##     combine, intersect,