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

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

--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

Jack Hou

Greg Puleo

Amin Emad

Jian Ma

Olgica Milenkovic