This code is available at https://github.com/aaronsk7/guppy-methylation
This script performs enrichment analysis of methylkit results.
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':
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## throw
## The following objects are masked from 'package:methods':
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## getClasses, getMethods
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## attach, detach, load, save
## R.utils v2.10.1 (2020-08-26 22:50:31 UTC) successfully loaded. See ?R.utils for help.
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## Attaching package: 'R.utils'
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## timestamp
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## cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
## warnings
library("parallel")
library("reshape2")
library("kableExtra")
library("dplyr")
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## Attaching package: 'dplyr'
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## group_rows
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## filter, lag
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## intersect, setdiff, setequal, union
library("RColorBrewer")
library("GenomicRanges")
## Loading required package: stats4
## Loading required package: BiocGenerics
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## Attaching package: 'BiocGenerics'
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## combine, intersect,