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:
Data sharing statement: see manuscript.
nohup Rscript scripts/01-sample_sheet.R > logs/01.log &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 &nohup Rscript scripts/08-ewas_finngedi.R > logs/08.log &
nohup Rscript scripts/08-ewas_finngedi_snps.R > logs/08_snps.log &nohup Rscript scripts/09-ewas_finngedi_h.R > logs/09.log &
nohup Rscript scripts/09-ewas_finngedi_h_snps.R > logs/09_snps.log &nohup Rscript scripts/10-ewas_finngedi_lmm.R > logs/10.log &
nohup Rscript scripts/10-ewas_finngedi_lmm_snps.R > logs/10_snps.log &nohup Rscript scripts/12-article.R > logs/12.log &nohup Rscript scripts/20210122-rebuttal.R > logs/20210122-rebuttal.log &nohup Rscript scripts/15-ewas_finngedi_lmm_rebuttal.R > logs/15.log &nohup Rscript scripts/16-ewas_finngedi_h_rebuttal.R > logs/16.log &nohup Rscript scripts/17-ewas_finngedi_rebuttal.R > logs/17.log &nohup Rscript scripts/18-article_rebuttal.R > logs/18.log &