AMTHet

Inferring intra-tumor hetoerogeneity using convex optimization and branch-and-bound search

Subdirectories:

• mixclone: Contains files to run MixClone on our data
  1. datagen: Code to generate synthetic data from corresponding input file for THetA
  2. run_mixclone.py: Code to run MixClone pipeline from commnand line
• ThetA_06_bootstrap: Part of ThetA 0.6 required for our experiments
  1. interval_files: Contain input files for THetA. Generated input files for THetA and MixClone are stored here.
  2. output: Output files from MixClone and THetA.
  3. PD4120a* files are used to run experiment on breast cancer sequencing data.

Files:

• alt_min_fn_upd.m: This function implements AMTHet.
• L_perm.m: Helper function for experiments
• synthdatagen_scnvsim.m: MATLAB script to generate input data for THetA with a process similar to SCNVSim.
• runMixClone_scnv.cmd: Windows batch script to run MixClone
• runTHeTA_MixClone_scnv.cmd: Windows batch script to run MixClone and THetA
• runTHeTA_n3k3_scnv.cmd: Windows batch script to run THetA
• runTHeTA_cancerseqdata.cmd: Windows batch script to run THetA on PD4120a
• synthreadres.m: MATLAB script to read results from MixClone and THetA and run AMTHet on corresponding input files
• readres_PD4120a.m: MATLAB script to read results from THetA and run AMTHet on PD4120a