This repository is forked from gerstung-lab/AML-multistage for our manuscript Validating the knowledge bank approach for personalized prediction of survival in acute myeloid leukemia: a reproducibility study.
/doc/SupplementaryMethodsCode.R is to present our modifications of the original code by Gerstung et al.. We modified the code in order to reproduce their published results in Gerstung M, Papaemmanuil E, Martincorena I, et al. Precision oncology for acute myeloid leukemia using a knowledge bank approach. Nat Genet. 2017;49(3):332-340. doi:10.1038/ng.3756.
For comparison purposes, modifications were only made when coding errors from the original R script prevented the continuation of the process.
We tailored the source code and performed a reanalysis for ‘concept testing’ purposes: to clarify the conflation between causal inference and predictive model in the original paper. The results are summarized in Fig. 3 in our manuscript.
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/reanalysis/Fig3.Ris to generate Fig. 3, which works on the same data in/dataas did in the original study. -
In addition, we provided a Docker image for our reanalysis: https://hub.docker.com/repository/docker/yujunxu/aml-multistage-reanalysis (built from
/reanalysis/Dockerfileand/reanalysis/install_packages.R, tested onDebian 11.0 64-bitandUbuntu 18.04 64-bit)- docker pull
docker pull yujunxu/aml-multistage-reanalysis:1.3 - docker run
docker run -it yujunxu/aml-multistage-reanalysis:1.3 /bin/bash
- docker pull