DNAmArray

• Script 1: Splitting Data
• Script 2: Saving sData for MethylAid
• Script 3: MethylAid and PCA
• Script 4: Checking genotypes with omicsPrint
• Script 5: Genotype checking for LLS
• Script 6: Genotype checking for GOTO
• Script 7: Sample corrections
• Script 8: Functional normalization
• Script 9: Probe-level QC
• Script 10: Descriptive tables
• Script 11: Non-response analysis

Skeletal Muscle

• Script 12: Base model
• Script 13: Clustering single nuclei data
• Script 14: Predicting nuclei-type proportions
• Script 15: Estimating changes in nuclei-types
• Script 16: Adjusted model
• Script 17: Volcano plot
• Script 18: DMRs and Homer
• Script 19: Chromatin state enrichment
• Script 20: Differentially expressed genes
• Script 21: eQTM analysis
• Script 22: Trait DNAm associations
• Script 23: Output dotplot figures

Subcutaneous Adipose

• Script 24: Base model
• Script 25: Estimating changes in cell-types
• Script 26: Volcano plot
• Script 27: DMRs and Homer
• Script 28: Chromatin state enrichment
• Script 29: Differentially expressed genes
• Script 30: eQTM analysis
• Script 31: Trait DNAm associations
• Script 32: Output dotplot figures

Fasted Blood

• Script 33: Base model
• Script 34: Predicting cell-type proportions
• Script 35: Estimating changes in cell-types
• Script 36: Volcano plot
• Script 37: DMRs and Homer
• Script 38: Chromatin state enrichment
• Script 39: Differentially expressed genes
• Script 40: eQTM analysis
• Script 41: Trait DNAm associations

Epigenetic Clocks

• Script 42: Prediction
• Script 43: dnaMethyAge
• Script 44: Bernabeu bAge prediction
• Script 45: Predicting MEAT from muscle DNAm
• Script 46: Plots and trait associations

Work in progress - add link to MedRXiv