alabarga / mnp_training

DNA methylation-based classification of central nervous system tumours

mnp_training

Collection of scripts used to train and validate the classifier presented in

DNA methylation-based classification of central nervous system tumours.

classifier training and cross validation

preprocessing.R

Reads raw data, performs normalization, basic filtering and batch effect adjustment. Normalized and filtered data is stored in ./results

training.R

Trains the Random Forest classifier and stores the final classifier in ./results

cross_validation.R

Performs nested cross-validation and stores the results in ./CV

calibration.R

Evaluates the results of the cross validation and fits the calibration model that is stored in ./results and compiles a final report showing classifier performance metrics CVresults.html.

tumor purity estimation

To train a Random Forest regression model that predicts ABSOLUTE purity of TCGA brain tumor samples, see purity.html or purity.Rmd