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Case control studies

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epzjlm edited this page Apr 22, 2025 · 1 revision

If you have a case-control design, we recommend to combine cases and controls for the mQTL analysis to have the largest sample size as possible. We do not recommend to analyse cases and controls separately.

Data preparation prior to pipeline

Pipeline set up

QC stage 01 (ready)

0. Set up folders
1a. Check data
1b. Process genetic data
1c. Check methylation and phenotypes
1d. mQTL control GWAS
1e. GWAS of genetic PCs
1f. Cross-cohort normalisation of methylation data
1g. Compute haplotype components
1 upload. Upload to Bristol SFTP

The pipeline modules (under development)

2a. Relatedness assessment/removal
2b. Regular and variance EWAS
3a. Run meQTL analysis
3b. Run variance meQTL analysis

Instructions for developers

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