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Longitudinal studies
If you have a cohort where methylation has been measured at multiple timepoints we would recommend that you split the study by timepoint.
For example if you have a study with methylation measured at age 7 and age 15 we recommend you name your study as $study_name_7 and $study_name_15 and run the analyses for each timepoint separately. Please note these should only include non-overlapping individuals.
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- System requirements and pipeline installation
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
2a. Relatedness assessment/removal
2b. Regular and variance EWAS
3a. Run meQTL analysis
3b. Run variance meQTL analysis