Repository navigation
bin
Directory actions
More options
Directory actions
More options
bin
Folders and files
| Name | Name | Last commit date | ||
|---|---|---|---|---|
parent directory.. | ||||
## Usage ##
./PLW <PPI_edge_list.txt> <Output_Clusters.txt>
## Example ##
./PLW ../inputData/ppi.dip.cleaned.txt clusters.txt
## Essential options ##
<position 1> PPI edge list (tab-delimited)
<position 2> Output cluster file location
--help Produce this help message
## Notes on OpenMP support ##
By default, PLW is able to take advantage of multi-core processors to speed
up the calculation of scores. Parallelisation support for the other calculations,
such as similarity calculation and core mining, is being explored and will be added
in the near future.
## Basic options ##
-u [ --seedselect_threshold ] arg
Fraction of Top-Ranked Nodes to use
as Seeds [0.0-1.0] [=0.3]
--randWalk_starting_energy arg Core - Random Walk - Starting Energy
[=2.0]
--randWalk_n_walks arg Core - Random Walk - No. of walks to
take [=100]
-C [ --core_threshold ] arg Core Mining Threshold (significance
level in term of sigma [=2.5758]
-P [ --dump_pcores ] arg Output processed cores to supplied filename
## Import / Export Data options ##
-l [ --load_similarities ] arg Similiarity Filename to preload
-L [ --load_scores ] arg Score Filename to preload
-C [ --dump_cores ] arg Output unprocessed cores to filename
-P [ --dump_pcores ] arg Output processed cores to supplied filename
-d [ --dump_similarities ] Dump similarities to stdout and exit
-D [ --dump_scores ] Dump scores to stdout and exit
## Advanced options ##
--similarity_method arg Similarity Method [cos*, cosW, none]
-s [ --score_method ] arg Scoring Method [1-8] [=1]
-c [ --core_method ] arg Core Method [randWalk*, coach]
-p [ --process_method ] arg
Processing Method [rfilter*, none]
-a [ --attachment_method ] arg
Attachment-Selection Method [coach*, EM,
cluster2PrtnLinks, none]
--randWalk_drop_power arg Core - Random Walk - Power to raise the
drop to [=1]
-b [ --belonging_threshold ] arg
Belonging Threshold for adding
Attachments [0.0-1.0] [=0.50]
-r [ --redundancy_threshold ] arg)
Redundancy Threshold for filtering
duplicate complexes [0.0-1.0] [=1.0]
-m [ --merging_threshold ] arg Merging Threshold for merging complexes
[0.0-1.0] [=1.0]
-v [ --verbose ] Verbose output for debugging