Enrichment Analysis

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':
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##     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':
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##     group_rows

## The following objects are masked from 'package:stats':
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##     filter, lag

## The following objects are masked from 'package:base':
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##     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,