spurthy111 / EpiSmokEr

Epigenetic Smoking status Estimator

EpiSmokEr: Epigenetic Smoking status Estimator

An R Package for the estimation of smoking status based on whole blood 450K methylation profiles

Features of EpiSmokEr

• Can perform smoking score calculation starting from idat files.
• Normalization of datasets using channel and colour specific quantile normalization.
• Smoking score calculation using three methods.
• Prediction of smoking status based on the whole blood methylation data.
• Results provided in html and csv format.

Installation

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)

Dependencies

EpiSmokEr depends on the following packages:

library(IlluminaHumanMethylation450kmanifest)
library(minfi)
library(htmlTable)
library(rmarkdown)

Vignette

Please refer to the vignette for step by step demonstration of functions in the EpiSmokEr package.