sebrauschert/dnasmoker

A R package to create a score for in utero exposure to maternal smoking, based on whole blood DNA methylation.

DNAsmokeR package

This package is based on the paper by

Rauschert S, Melton PE, Heiskala A, Karhunen V, Burdge G, Craig JM, Godfrey KM, Lillycrop K, Mori TA, Beilin LJ, Oddy WH, Pennell C, Jaervelin MR, Sebert S, Huang RC. Cross-Continent Poly-DNA Methylation Score for Fetal Exposure to Maternal Smoking, developed in adolescents with Machine Learning Methods. in preparation.

It contains a function to create a whole blood DNA methylation in utero exposure score to maternal smoking during pregnancy.

Installation

This package can be installed in its BETA version by typing the following into the R console:

devtools::install_github("Hobbeist/DNAsmokeR", build_vignettes=T)

Functions

This package currently contains four functions:

• smokeScore()
• scoreMatrix()
• boxplotScore() , and
• shinySmokeR()

More details on these functions can be found in the vignette of this package and in the help pages in R.

dnasmoker's Issues

Feedback message on missing CpGs

Some studies might not have all CpGs available, hence I will implement a feedback message with the list of CpGs that are missing as compared with the coefficients from the model. Therefore the user can report that the score is an approximation and also add the missing CpGs to the report.

Shiny interface

Implement a shiny interface for ease of use.

Implement a report generation option

For LifeCycle project validation purpose.