btclusterer

Clusters purification bootstrap samples using the Markov Clustering algorithm. Scans over a specific range of inflation coefficient parameters.

This tool implements the only time-consuming step of bootstrap scores network calculation. It can be used to parallelize the calculation process by clustering only a small set of purification data samples for each call. Use btfinisher to merge the results and calculate the final bootstrap network and complexes.

Call the tool without any command line arguments to get detailed information about the parameters for this program.

See also: Score network generation

Example calls

These examples tie in with the bootstrap sample generation example from btsampler. They assume an existing output directory btresults/ in the current working directory.
./cmdline.sh btclusterer -i gavin_1000_samples -s 1-10 -inf 2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 -c 5 -prefix btresults/bt_ ./cmdline.sh btclusterer -i gavin_1000_samples -s 11-20 -inf 2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9 -c 5 -prefix btresults/bt_

and so on...

For each sample one network and one clustering file will be generated in the output directory.


ProCope documentation