/HSCT-relapse-model

Genomic prediction of relapse after HSCT

Primary LanguageRGNU General Public License v3.0GPL-3.0

HSCT-relapse-model

This repository contains the scripts for feature selection and RF model fitting for prediction of relapse after HSCT as described in the publication:

Ritari J, Hyvärinen K, Koskela S, Itälä-Remes M, Niittyvuopio R, Nihtinen A, Salmenniemi U, Putkonen M, Volin L, Kwan T, Pastinen T, and Partanen J (2018). Genomic prediction of relapse in recipients of allogeneic haematopoietic stem cell transplantation. Leukemia. 2018 Aug 8. doi: 10.1038/s41375-018-0229-3.

code (./src)

Plink_feature_selection.sh Shell script for Plink association test leaving each sample out in turn.

RF_relapse.R R script for Random Forest fitting and prediction using the same folds as in Plink variant selection (above).