README

Information for compiling and running the NetSig binary

To run the code, just compile:
g++ -O3 runNetwork.cpp -o runNetwork

and run:
./runNetwork -p input/pvals -j 1 -J 1 -n input/network.sym -N test -i 1000 -P 3 -g -o .

To compile for multiple threads:
g++ -O3 -fopenmp runNetwork.cpp -o runNetwork

Compiling Notes:
Under MacOXX, as clang is the default compiler, the compilation will likely fail. Pleas use gcc (install using MacPorts, Fink etc.)
Also, using gcc5 will increase the performance significantly. 

Please use the --help parameter to see how to run NetSig.

A short explanation for some of the parameters used in the test run is given below.
runNetwork -p input/pvals -j 1 -J 1 -n input/network.sym -N test -i 1000 -P 3 -g -o .
-p input/pvals
specifies the file for the p-values. Found in the input directory these are from the Lawrence et al. manuscript referenced in the manuscript.
-n input/network.sym
specifies the network (in this case InWeb 3) to use
-j, -J
this is the lazy mens way of parallelizing. -J defines the number of jobs to run, -j tells the script which job it has to process.
So for running three jobs in parallel, one would submit three the following two jobs:
runNetwork -p input/pvals -j 1 -J 3 -n input/network.sym -N test -i 1000 -P 3 -g -o .
runNetwork -p input/pvals -j 2 -J 3 -n input/network.sym -N test -i 1000 -P 3 -g -o .
runNetwork -p input/pvals -j 3 -J 3 -n input/network.sym -N test -i 1000 -P 3 -g -o .
this will create three result files which can be easily joined.
-N test
This sets the name for the job, used in the result file for identification
-i 1000
This sets the number of iterations, defining the miuimal p-Value that can be caluclated (1/iterations)
-P 3
The column index in the p-Value file that should be used. Please note that the first column has index 0 (so so 3 corresponds to column 4)
The file should be tab-seperated
-o
The output directory for result files.

#Tab seperated network into sif format
gawk '(ARGIND==1){a[$1]=$2}(ARGIND==2){if($1 in a){if($2 in a){print a[$1]"-"a[$2]}}}' InWeb3.HUGO.mapping network.sym > a.sif

#Another example for running a binary network with mapping file:
runNetwork -p input/pvals -j 1 -J 1 -n input/network0.bin -N test -i 1000 -P 3 -g -o . -M input/InWeb3.HUGO.mapping -V -C