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.
Install the needed R packages
RScript install/installRLibs.R