License: SharmaLab - Channing Division of Network Medicine
To better use the package install "pip" and "python 2.7"
TO INSTALL: sudo pip install confine
PACKAGE REQUIREMENTS: The code can install all required packages for you.
- pickle
- networkx
- os
- time
- pylab
- pkg_resources
To INSTALL PACKAGES:
- call python
- import confine
- confine.check()
To TEST:
- call python
- import confine
- confine.run('test')
INPUT FORMAT: it should be either in csv or txt format. It includes 2 Comma-delimited columns in which the first column is reserved for gene id and the second is reserved for corresponding gene p.value.
OUTPUTS:
- a text file that includes gene id and gene symbol of LCC.
- a png file that shows how the significance of LCC varies with P.value cut-off over LCC thresholds given by user. directory: Outputs are being generated at directory where the user is running python
TO RUN:
- call python
- import confine
- confine.run('optional_name')
- Answer 1st question "Enter your file name located at INPUT folder: " path/filename
- Answer 2nd question Enter the minimum size of LCC, we recommend a number between 30 and 50: " 50
- Answer last question Enter the maximum size of LCC, we recommend a number between 300 and 500: " 400
TO ACCESS OUTPUT FILES: two output files are being generated in a directory that is names the same as 'optional_name' followed by a unique number.
GOAL: Identifying the most significant region of connections between disease-related proteins with a limited size by user.