Prediction of AML development in healthy individuals

This repository contains code accompanying Prediction of AML risk in healthy individuals by Abelson, Collord, et al. (2018), Nature, 559:400-404. http://dx.doi.org/10.1038/s41586-018-0317-6.

All code is contained in preAML.R with the corresponding output in preAML.html.

Requirements

The script was run in R versions 3.4.1 and 3.5.1.

install.packages(c("survAUC","survivalROC","stringr","dplyr","readr","devtools","ROCR","rmarkdown"))
devtools::install_github("gerstung-lab/CoxHD/CoxHD@bc60c16")
devtools::install_github("mg14/mg14@6a63283")

Necessary data files are contained in the data directory.

Run

The provided output has been generated in R-3.5.1 from the toplevel directory using the command

rmarkdown::render("preAML.R")`

The typical run time is about 2h, using 4 cores, the longest part is section 7.4.8, which may be omited by commenting out the corresponding sections in preAML.R.