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Significance clustering


Author:
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Martin Rosvall

For contact information, see 
http://www.mapequation.org/about


Getting started:
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In a terminal with the GNU Compiler Collection installed,
just run 'make' in the current directory to compile the
code with the included Makefile.

Call: ./sigclu [-s <seed>] [-c <confidencelevel>] [-w <weightsfile>] partitionsfile signodeoutfile sigmoduleoutfile
seed: Any positive integer.
confidencelevel: The confidence as a fraction, default is 0.95.
partitionsfile: Each column represents a partition, the first for the raw partition and the remaining for bootstrap partitions. Row number corresponds to node id.
nodeoutfile: 1 or 0 if a node does or does not belong to the significant core of its module.
moduleoutfile: moduleId1 moduleId2 means that the significant core of moduleId1 cooccurs with moduleId2 more than a fraction 1 - conf of the samples.
weightsfile: One column for weights of each node.  Row number corresponds to node id.

Example:

./sigclu -s 34 -c 0.95 -w weightsfilesample.txt partitionsfilesample.txt signodeoutfilesample.txt sigmoduleoutfilesample.txt

partitionsfilesample.txt
1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1
1 2 1 2 1 2 1 2 1 2 2
2 2 1 2 1 2 1 2 1 2 2
2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2
3 2 2 2 2 2 2 2 2 2 2
3 3 3 3 3 3 3 3 3 3 3
3 3 3 3 3 3 3 3 3 3 3

weightsfilesample.txt
1
1
2
2
3
3
4
4
5

signodeoutfilesample.txt
# First column: 1 in significant core, 0 otherwise. Second column: the relative co-clustering with significant core nodes over all bootstrap clusterings
Significant SignificantScore
0 0.4
0 0.4
1 1
0 0.6
1 1
1 1
0 0
1 1
1 1

sigmoduleoutfilesample.txt
# moduleId1 moduleId2 means that the significant core of moduleId1 cooccurs with moduleId2 more than a fraction 1 - conf of the samples.
1 2