This repository includes the workflows and additional tools for analyzing methylation data obtained from Infinium Methylation EPIC BeadChip and Infinium Mouse Methylation Beadchip Illumina arrays with R.
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R/MethylationEPIC.R: Workflow to analyze human methylation array data from the Illumina Infinium Methylation EPIC BeadChip.
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R/MouseAnnotation.R: Script to generate the manifest and annotation files required in MouseMethylation.R.
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R/MouseMethylation.R: Workflow to analyze mouse methylation array data from the Illumina Infinium Mouse Methylation BeadChip.
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R/plotDMR.R: Script to represent the obtained DMRs with a heatmap of the methylation values and their genomic location.
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data/ann_NCBI_mouse.csv: File generated with MouseAnnotation.R including the NCBI annotation of each probe present in the Mouse Methylation array.
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data/ann_UCSC_mouse.csv: File generated with MouseAnnotation.R including the UCSC annotation of each probe present in the Mouse Methylation array.
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data/enhancers_human.csv and data/enhancers_mouse.csv: Files including FANTOM5 enhancers annotated for human and mouse.
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data/manifest_mouse.csv: Manifest file for the Mouse Methylation array that maps the probes with their genomic position. It was generated with MouseAnnotation.R.
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docs/MethylationEPIC.md: Markdown version of MethylationEPIC.R.
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docs/refs/: Folder including the referenced figures.
During the analysis, I developed a package including some functions used in the workflow: methtools.
Raúl Sanz (2022)