PAM50 Classifier for Prostate Cancer.

This classifier is based on Zhao el al on JAMA for the microarray data, and if you have error or question for this code, let me know.(NOT PAPER)

Reference

Associations of Luminal and Basal Subtyping of Prostate Cancer With Prognosis and Response to Androgen Deprivation Therapy

Example

import pandas as pd
from cls.PAM50_classifier import PAM50_CLS

# Expression data has to be median centered and EntrezID indexed
df = pd.read_csv('cls/dataset/example_expr.csv', index_col=0)

# score_softmax = True : It means desicision score will be calculated to softmax(0~1).
# If it is False, score will be just correlation score
pam50 = PAM50_CLS(df, score_softmax=True)


print pam50.pam50_result ### Predicted result
print pam50.pam50_score ### Decision score of predicted result