emreg00 / proximity Goto Github PK

Hi Emre,
I have just read your wonderful work "Network-based in silico drug efficacy screening. Nat. Commun. 7:10331" and try to reproduce your codes.
I see you calculate the AUC in proximity.ipynb with list of -d$z and the list of ytrue in R script. I just wonder if the threshold of Z（-0.15）mentioned in the article should be used to judge the ypred(if z value <=-0.15 ypred=1，else ypred=0).
Thanks for your time!
Best wishes

Ze

Hi Emre,

First of all congratualtions for your great job, is really impressing. Now I'm contacting to you, because I read the paper "Network-based in silico drug efficacy screening" where you calculate the proximity between nodes using different formulas such as closest, shortest, kernel, centre,And also reference distance distribution, among others.

I'm interesting to calculate the closest and reference distance distribution and as far as I know I need the proximity package of this github. The problem remains about to know, which output is the closest and reference distance distribution, they are d and z respectively? I have my target drug nodes and disease nodes, and I want to calculate their proximity in order to know if my drug could potentially treat my disease.

Besides, how can I create the proximity.dat, proximity_similarity.dat and palliative.csv files to execute with my data the proximity.ipynb file?

THanks for your time

Jordi

i installed all packages and environments.

there is some problem. is this a sample code?

It looks like a part of some full code.