/EWAS_GreenSpace_Blood_2024

Green space exposure and blood DNA methylation at birth and in childhood – a multi-cohort study

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Green space exposure and blood DNA methylation at birth and in childhood – a multi-cohort study

In this GitHub, you will find scripts for the analyses performed in this study.

  • The cohort-specific epigenome-wide association studies (EWAS): You will find the scripts used in local (limma R package) (Ritchie et al., 2015) and through Data Aggregation Through Anonymous Summary-statistics from Harmonised Individual-level Databases (DataSHIELD) (dsOmics R package).

    • LC-LIT-ATH-EWAS-GreenSpaces-Cordblood_NoDataShield_code_v2.R
    • LC-LIT-ATH-EWAS-GreenSpaces-Childhood_NoDataShield_code_v2.R
    • LC-LIT-ATH_EWAS-GreenSpaces-DataShield.R

  • Example in the main model of the Quality control (QC) of the cohort-specific results using the EASIER R package.

    • QC_GS_CordBlood_M3.R
    • QC_GS_Child_Blood_M3.R

  • Example in the main model of the fixed-effects inverse variance-weight meta-analyses using the using the EASIER R package

    • MA_GS_CordBlood_M3.R
    • MA_GS_ChildBlood_M3.R

  • Example in the main model of the leave-one-out analysis, in which we re-ran the main analysis repeatedly with one of the cohorts removed each time

    • LOO_GS_CordBlood.R
    • LOO_GS_ChildBlood.R

  • Example in the in cord blood main model of the Differentially methylated regions (DMRs) using DMRcate R package and Enmix-combp R package on the meta-analysed results.

    • DMR_GS_CordBlood_M3.R