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Differential methylation and mQTL analysis of cartilage tissue in the developing knee joint

Workflow

This repository contains the code required to reproduce the bioinformatics analysis of the methylation and genotyping arrays.

01_Methyl_Preprocess.Rmd
Quality control and normalisation of the EPIC methylation arrays

02_Methyl_EDA.Rmd
Principal component analysis of the methylation data

03_Methyl_Differential.Rmd
Differential methylated site and region analysis

04_DMR_mFuzzClustering.Rmd
Mfuzz clustering of CpGs and enrichment analysis

05_processROADMAP.Rmd
Overlap of DMRs with ROADMAP chondrocyte chromatin states and ATAC-seq data

06_DMR_TFMotifs.qmd
Enrichment anaylsis of transcription factor motifs in DMRs

07_genotype_arrays.Rmd
Genotyping array processing (using bash scripts), quality control and identification of GWAS OA SNP LD proxies

08_matrixQTL_prep.Rmd
Preparation of methylation and genotyping data for mQTL analysis

09_matrixQTL_analysis.Rmd
Identification and plotting of mQTLs

10_mQTLComparisons.qmd
Comparison of the mQTLs against existing mQTLs from foetal brain and comparison of CpGs in the developmental DMRs vs the mQTLs.

11_Colocalisation.qmd
Colocalisation of the mQTL SNPs with osteoarthritis GWAS data

All Rmd and qmd files can be rendered within RStudio.

Installation

Install the needed R packages

RScript install/installRLibs.R