ewascombpr

A line that pipes epimedtools DNA methylation study to an ewas then to combp.

Prerequisits

Comb-p (https://github.com/brentp/combined-pvalues) need to be installed and launchable using comb-p command line call.

bioconductor packages needs to be installed:

BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19")
BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")

Quick launch

Under your terminal

cd ~/projects
git clone https://github.com/fchuffar/ewascombpr.git
cd ewascombpr/vignettes
R

Under R

# build Hannum 2013 study
rmarkdown::render("vignettes/01_build_study_geo.Rmd")
# run pipeline
rmarkdown::render("vignettes/02_ewas_combp.Rmd")

Usage

cd ~/projects/ewascombpr/

# push scripts on the server
rsync -auvP ~/projects/ewascombpr/ cargo:~/projects/ewascombpr/

# build GSE40279 methylation study
echo 'rmarkdown::render("vignettes/01_build_study_geo.Rmd")' | Rscript -

# analyse GSE40279 methylation study (meth~age+gender)
echo 'rmarkdown::render("vignettes/02_ewas_combp.Rmd")' | Rscript -

# build and analyse GSE40279 methylation study with sankemake
cd vignettes/
snakemake -s wf.py -pn