Tumor Heterogeneity Extensible Modeling via an Integrative System
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bin
data
doc
model/jointAnalysisAuto
src
tutorial
LICENSE
README.md
_config.yml

README.md

File organization

Source code (under ./src/): java code for file generation

  • generatingGausianMeansAL5Copies.java // generate Gaussian means for different genotypes and prevalence levels
  • generatingGausianMeansAL5CopiesNoCNAs.java // generate Gaussian means for different genotypes and prevalence levels when there is no CNA event
  • updateOffDiagonalElementsForEMUntieVariances.java // update the diagonal elements in the transition matrices and process the input as the required format for GMTK, this piece of code is used for joint analysis of multiple biopsies
  • updateOffDiagonalElementsForEMUntieVariancesIndividualAnalysis.java // update the diagonal elements in the transition matrices and process the input as the required format for GMTK, this piece of code is used for individual biopsy analysis
  • generatingModelSpecificationFilesJointAnalysis.java // generate model specification files for multiple biopsy joint analysis
  • generatingModelSpecificationFilesIndividualAnalysis.java // generate model specification files for individual biopsy analysis
  • llRat.py // compare log-likelihood with that from last iteration

Dataset (under ./data/):

Example dataset used by THEMIS is combinedData_01-1-B2_01-2-B2_01-4-B3.txt

Documentation (under ./doc/):

The documentation of the source code and model specification files are provided in doc.md

Model specification files (under ./model/):

  • individualAnalysisAuto // a directory for performing individual biopsy analysis
  • jointAnalysisAuto // a directory for performing multiple biopsy joint analysis
  • structure.txt // a text file which specifies a candidate phylogenetic structure in joint analysis

Executables (under ./bin/): shell script for performing analysis

  • trainTestIndividualAnalysisAuto.sh // contains the script for individual biopsy analysis.
  • trainTestJointAnalysisAuto.sh // contains the script for multiple biopsy joint analysis.

Tutorial (under ./tutorial/)

A tutorial for replicating our analysis on the sample dataset is provided in tutorial.md

Directory/file explanation is provided in readme.md

Our manuscript can be accessed via http://biorxiv.org/content/early/2017/04/06/125138