Mendelian Randomization for Calcium-Cholesterol

[davebridges]

This required IRB approval to start (https://github.com/BridgesLab/GrantApplications/issues/12). Key steps include

• Instrument QC table (pre)
• Expand SP2 & Flow chart counts
• Harmonise (produce harmonised table) → write harmonised SNP table (step 4)
• Recompute per-SNP R² & F on harmonised set and write post-harmonisation QC table (step 4)
• Scatter plot (step 5)
• MR estimates table + forest (steps 6–7)
• Heterogeneity + pleiotropy + funnel (steps 8–9)
• LOO + radial / MR-PRESSO if needed (steps 10–11)
• Steiger summary + proxies table (steps 12–13)
• Bidirectional summary figure/table (step 14)
• Write supplement SNP table (step 15)