SRF which stands for Subtyping through Ranked Factorisation is an algorithm for finding cancer subtypes and subtype specific features by integrating mutation data, expression data and biological networks.
- Linux/Unix
- Scala
- Java
- Gurobi solver (http://www.gurobi.com/)
- OscaR (https://bitbucket.org/oscarlib/oscar/wiki/Home)
For support using SRF, please contact thanh.levan@cs.kuleuven.be
For best performance, install a Fortran or C complier and run one of the following commands (or some appropriate variation of them) prior to running HotNet for the first time:
SRF uses Gurobi to solve the optimisation problem. Hence, before running SRF, make sure that Gurobi is installed and its enviroment variables are setup correctly.
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| PARAMETER NAME | DEFAULT | DESCRIPTION |
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|-df | None |Absolute path to the tab-separated ranked diffusion file |
| | |where each row contains |
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|-ef | None |Absolute path to the tab-separated ranked expression file |
| | | |
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|-if | None |Initialised matrix F obtained by a hierarchical
| | |clustering. |
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|-k | 5 |Number of ranked factors |
| | | |
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|-etheta | 0.65 |Rank expression threshold (\theta_2 in the paper) |
| | |Remember that it is a number in the range of [0..1] |
| | |The actual integer threshold that is used in the program is |
| | |calculated as followed: \theta_2 * n, where n is the number |
| | |of the columns of the rank matrix. |
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|-dtheta | 0.86 |Rank diffusion threshold (\theta_1 in the paper) |
| | |Remember that it is a number in the range of [0..1] |
| | |The actual integer threshold that is used in the program is |
| | |calculated as followed: \theta_1 * maxD, where maxD is the |
| | |user-input value specifying the maximum value of rank |
| | |diffusion. |
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|-beta | 1 |The rank imbalance threshold used to specify the relative
| | |importance between mutation data and expression data. |
| | | |
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|-k | 5 |Number of ranked factors |
| | | |
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|-nReqMut | 2 |Number of required mutations |
| | | |
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|-maxD | 0 |Maximum value of ranked diffusion. This should be equal to |
| | |the number of vertices in the graph used to run the |
| | |diffusion. Note that if maxD = 0, the program |
| | |uses the number of rows of the ranked diffusion matrix |
| | |the maximum value of ranked diffusion. |
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|-maxE | 0 |Maximum value of ranked expression. This should be equal to |
| | |the number of the columns of the ranked expression |
| | |matrix. Note that if maxE = 0 or is not specified, |
| | |the program automatically uses the number of the columns |
| | |of the ranked expression matrix the maximum value of ranked | | | |expression. |
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|-dir | ./ |Working directory which will be used to store the results |
| | | |
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|-log | false |Log intermediate results into files |
| | | |
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If you use SRF in your work, please cite:
T. Le Van, M. van Leeuwen, ..., L. De Raedt, K. Marchal, S. Nijssen. (2016) Simultaneous discovery of cancer subtypes and subtype features by molecular data integration. Bioinformatics, ?, (2016).