Please cite our 2013 publication when using this work:
Wagner, A. H. et al. Prioritization of retinal disease genes: an integrative approach. Hum Mutat 34, 853-859, doi:10.1002/humu.22317 (2013).
Here is a compiled and packaged version of our code for our project. This runs the logistic regression method for producing probabilities for each gene. The output could then be redirected into a text file and then sorted in decreasing order of probabilities to get the ranking.
Feature vectors are for the training of a retinal degenerative disease model, as described in our paper. Classifier results are from training features.csv using PULP with the respective regression function.
Usage:
java -jar -Xmx2G CG_Method_LogisticRegression.jar features.csv
OR
java -jar -Xmx2G CG_Method_LogisticRegression.jar features.csv > output.csv