An R Package for the estimation of smoking status based on whole blood 450K methylation profiles
- Can perform smoking score calculation starting from idat files.
- Normalization of datasets using channel and colour specific quantile normalization.
- Prediction of smoking status based on the whole blood methylation data.
- Results provided in html and csv format.
EpiSmokEr depends on the following packages:
library(IlluminaHumanMethylation450kmanifest)
library(minfi)
library(htmlTable)
library(rmarkdown)
To install EpiSmokEr, start R and then type the following commands:
source("http://bioconductor.org/biocLite.R")
install.packages("devtools") # if you don't have the package, run install.packages("devtools")
library(devtools)
install_github("sailalithabollepalli/EpiSmokEr")
library(EpiSmokEr)
Please refer to the vignette for step by step demonstration of functions in the EpiSmokEr package.
If you use EpiSmokEr, please cite:
Bollepalli S, Korhonen T, Kaprio J, Anders S, Ollikainen M. EpiSmokEr: a robust classifier to determine smoking status from DNA methylation data. Epigenomics. 2019 Oct;11(13):1469-1486. doi: 10.2217/epi-2019-0206. Epub 2019 Aug 30. PMID: 31466478.