This repository documents the code used to analyze the data for "Cord Blood DNA Methylation of Differentially Methylated Regions Associates with Infant and Child adiposity”
Methylation data underwent QC/preprocessing with the minfi pipeline, detailed in minfi_qc.R.
Combat was used for batch correction by sample plate (7 plates total), detailed in combat_byPlate.R
Methylation data was batch corrected using combat prior to analysis. We show the adequacy of this correction with MDS plots of probes by plate before and after correction in QC_combatCorrections/
Code used for analysis are detailed under analysisCode/
This code is generalized here, but was run for each of the outcomes of interest (changes in adiposity across the 3 timepoints, pairwise)
Analysis proceeded in the following order:
- ewas_code.R (includes function defined in ewas_fun.R)
- combp_setup.R
- combp_analyses.sh
- clean_combp.R (includes function defined in methyl_dir_fun.R)
Session information for these analyses are detailed in analysis_sessionInfo.md