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
EX_CO_ME
positive weight being EX (expression) and CO (coverage)NI_CO_ME
positive weight being NI (expression) and CO (coverage)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