umr1283 / epxgdm

Scripts for 'Epigenome Wide Association Study Reveals Methylation Loci Associated with Offspring Gestational Diabetes Mellitus Exposure and Maternal Methylome'

EpxGDM

This repository contains all scripts used to perform the analyses described in the manuscript entitled: "Epigenome Wide Association Study Reveals Methylation Loci Associated with Offspring Gestational Diabetes Mellitus Exposure and Maternal Methylome" from Canouil et al., 2021 (doi: 10.2337/dc20-2960)).

Scripts were executed using the following Docker images stored on Docker Hub:

• umr1283/stat:R403
• umr1283/stat:4.0.4

Data sharing statement: see manuscript.

Design

nohup Rscript scripts/01-sample_sheet.R > logs/01.log &

Quality-Control EPIC Array

nohup Rscript -e 'rmarkdown::render(input = here::here("scripts", "02-qc_idats.Rmd"), output_file = "EpxGDM_EPIC_QC.html", output_dir = here::here("reports"), encoding = "UTF-8", intermediates_dir = here::here("outputs", "02-qc_idats"), params = list(output_directory = here::here("outputs", "02-qc_idats")))' > logs/02.log &

nohup Rscript -e 'rmarkdown::render(input = here::here("scripts", "02-qc_idats_snps.Rmd"), output_file = "EpxGDM_EPIC_QC_SNPs.html", output_dir = here::here("reports"), encoding = "UTF-8", intermediates_dir = here::here("outputs", "02-qc_idats_snps"), params = list(output_directory = here::here("outputs", "02-qc_idats_snps")))' > logs/02_snps.log &

Statistical Analyses (FinnGeDi)

Perform EWAS for GDM

nohup Rscript scripts/08-ewas_finngedi.R > logs/08.log &

nohup Rscript scripts/08-ewas_finngedi_snps.R > logs/08_snps.log &

Perform 'heritability' EWAS for GDM

nohup Rscript scripts/09-ewas_finngedi_h.R > logs/09.log &

nohup Rscript scripts/09-ewas_finngedi_h_snps.R > logs/09_snps.log &

Perform 'LMM' EWAS for GDM

nohup Rscript scripts/10-ewas_finngedi_lmm.R > logs/10.log &

nohup Rscript scripts/10-ewas_finngedi_lmm_snps.R > logs/10_snps.log &

Article

Materials

nohup Rscript scripts/12-article.R > logs/12.log &

Rebuttal

Main Comments Checks

nohup Rscript scripts/20210122-rebuttal.R > logs/20210122-rebuttal.log &

Perform 'LMM' EWAS for GDM with primipara and/or mumwtgain

nohup Rscript scripts/15-ewas_finngedi_lmm_rebuttal.R > logs/15.log &

Perform 'heritability' EWAS for GDM

nohup Rscript scripts/16-ewas_finngedi_h_rebuttal.R > logs/16.log &

Perform EWAS for GDM

nohup Rscript scripts/17-ewas_finngedi_rebuttal.R > logs/17.log &

Article Materials

nohup Rscript scripts/18-article_rebuttal.R > logs/18.log &