clusterer
This tool clusters a given scores network and writes the resulting
clustering to the standard output or into a file.
Call the tool without any command line arguments to get detailed
information about the parameters for this program.
See also:
Example calls
- cluster the bootstrap scores network (
-net
)
- use the MCL algorithm (
-method mcl
)
- clustering coefficient: 2.5 (
-I
)
- write to file instead of standard output (
-o
)
- do not include singletons (clusters consisting of just one protein) in the results (
-nosingle
)
cmdline.sh clusterer -net data/scores/bootstrap_combined.txt.gz -method mcl -I 2.0 -o mcl.out -nosingle
- same setup but this time use hierarchical clustering (
-method hcl
)
- linkage method: UPGMA (
-linkage
)
- cut-off value: 0.2 (
-cutoff
)
cmdline.sh clusterer -net data/scores/bootstrap_combined.txt.gz -method hcl -linkage upgma -cutoff 0.2 -o hcl.out -nosingle