Skip to content
master
Switch branches/tags
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 

C3

This is the readme file for C3 and its usage and parameters

Usage

C3 is a python script, and it can be run as a python script using the format python c3Method.py --cancer --filter --percentile --up --down --J_percentile --alpha --date --a --bound --cond --address --output --c --network

Arguments

--cancer this is the cancer argument, or more or less your output tag

--filter this argument is a filters the minimum number of times a gene can be altered to count towards C3. Default value is 20

--percentile a similar argument to filter, it filters only the top percentile of genes by alteration frequency. It acts as a secondary filter paramter in lieu or combined with filter to select altered genes. Default value is 90.

--up an argument that determines the upper threshold for a GISTIC copy number signal to count as significant. Default is 3

--down an argument that determines the lower threshold for a GISTIC copy number signal to count as significant. Default is -1

--J_percentile the J_percentile 4 Default value is 90.

--alpha the alpha argument. The default argument is 0.29.

--date the date argument (for labelling purposes). The default date is April 29 (the date our project started :) )

--a the a argument. The default argument is 4

--bound the argument that indicates the upward bound for the cluster size. Default is 5

--cond which positive and negative weights do you address. ME is always a negative weight, so this argument determines the positive weights. We currently support

  1. EX_CO_ME positive weight being EX (expression) and CO (coverage)
  2. NI_CO_ME positive weight being NI (expression) and CO (coverage)
  3. triple using NI, EX and CO as separate weights

--address the address you use as your working folder where your files are

--output the address of your destination folder

--c This determines the weight of the first parameter in the case of a EX_CO_ME or NI_CO_ME weighting scheme

--network the destination of your network folder (if applicable)

--cov the weight of your coverage parameter. Only used if --cond is triple. Default is 0.33

--exp the weight of your expression parameter. Only used if --cond is triple. Default is 0.33

--net the weight of your network parameter. Only used if --cond is triple. Default is 0.33

Credits

Jack Hou

Greg Puleo

Amin Emad

Jian Ma

Olgica Milenkovic

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages