https://github.com/swiri021/PAM50_Classifier_for_PRCA

PAM50 classifier for Prostate Cancer in Python
https://github.com/swiri021/PAM50_Classifier_for_PRCA

pam50 pam50classifier prad prostate-cancer

Last synced: 2 months ago
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PAM50 classifier for Prostate Cancer in Python

• Host: GitHub
• URL: https://github.com/swiri021/PAM50_Classifier_for_PRCA
• Owner: swiri021
• Created: 2019-01-22T21:02:06.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2019-08-23T17:31:48.000Z (over 5 years ago)
• Last Synced: 2024-08-04T10:01:30.059Z (6 months ago)
• Topics: pam50, pam50classifier, prad, prostate-cancer
• Language: Python
• Homepage:
• Size: 471 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-ai-cancer - swiri021/PAM50_Classifier_for_PRCA - [[Paper](https://jamanetwork.com/journals/jamaoncology/article-abstract/2626510)] - PAM50 classifier for prostate cancer in Python based on Zhao el al on JAMA for the microarray data (Code / Repositories)

README

        
# 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](http://jamanetwork.com/journals/jamaoncology/article-abstract/2626510)

# Example

```Python

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

```