Activation level of 64 gene signatures in glioblastoma

This repository includes the XGBoost models and the R scripts to infer the activation status of 64 gene signatures in GBM, as published in this manuscript:

Topographic mapping of the glioblastoma proteome reveals a triple axis model of intra-tumoral heterogeneity
Lam KHB, Leon AJ, Hui W, Lee SCE, Batruch I, Faust K, Koritzinsky M, Richer M, Djuric U, Diamandis P (under review)

The models take as input proteomics (LFQ) of rna (TPM) expression data.

Execute the following command to analyze the sample data:

Rscript predictXGB.R --data sample/sample_prot.rds \
                     --models data/list_xgb-gbm_64_signatures-prot-v01.RData \
                     --out_csv predictXGB_sample_rna.csv