Nimbus

Nimbus is a Ruby gem that implements Random Forest in a genome-wide prediction context. Nimbus trains the algorithm based on an input file (learning sample) containing the phenotypes of the individuals and their respective list of genotype markers (i.e. SNPs). A random forest is created and stored in a .yml file for future use. Nimbus can also be run to make prediction in a validation set or in a set of data containing yet to be observed response variable. In this case, the predictions can be obtained using the random forest created with a learning sample or with a previously stored random forest. If a learning sample is provided, the gem will create a file with the variable importance of each feature (marker) in the data. The higher the importance is, the more relevant the marker is to correctly predict the response variable in new data. Nimbus can be use for both classification or regression problems, and the user may provide different parameter values in a configuration file to tune the performance of the algorithm.