Difference between revisions of "Construct composite modules (analysis)"

Revision as of 12:17, 12 April 2013

Predict composite module using site search on genes result

Site search result – Result of previous site search run with background track
Genetic algorithm parameters (expert) – Genetic algorithm parameters
- Number of iterations – Number of iterations
- Population size – Population size
- Non-change limit – Number of iterations to stop after if best score is not improved
- Elite size – Number of elite organisms (i.e. best organisms to survive unconditionally)
- Mutation rate – This controls how often mutation occurs and how significant they are (0..1)
Parameters (expert) – Parameters
- Penalty rate – Which penalty value will be assigned
- Site models in focus – At least one of these models must present in the resulting composite model to have non-zero score
Model parameters – Model parameters
- Min modules – Minimal number of modules
- Max modules – Maximal number of modules
- Gaussian model (expert) – Gaussian model
  - Min models – Minimal number of site models in module
  - Max models – Maximal number of site models in module
  - Min sites to account – Minimal number of sites to account
  - Max sites to account – Maximal number of sites to account
  - Min module width – Minimal width (sigma) of the module
  - Max module width – Maximal width (sigma) of the module
Output path – Path to store result

@@ Line 10: / Line 10: @@
 ** '''Elite size''' – Number of elite organisms (i.e. best organisms to survive unconditionally)
 ** '''Mutation rate''' – This controls how often mutation occurs and how significant they are (0..1)
+* '''Parameters''' (expert) – Parameters
 ** '''Penalty rate''' – Which penalty value will be assigned
+** '''Site models in focus''' – At least one of these models must present in the resulting composite model to have non-zero score
 * '''Model parameters''' – Model parameters
 ** '''Min modules''' – Minimal number of modules