Construct composite modules on track (correlation) (analysis)
From BioUML platform
- Analysis title
- Construct composite modules on track (correlation)
- Provider
- geneXplain GmbH
- Class
CMACorrelationOnTrack
- Plugin
- biouml.plugins.cma (Composite module analyst)
Parameters:
- Experiment track – Path to experiment ('yes') track
- Correlation column – Column to correlate with
- 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)
- Score calculation parameters (expert) – Parameters which control score calculation
- 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
- Site models in focus table (expert) – The table of site models in focus
- All modules contain site model in focus – If checked, then each module must contain at least one site model from the focus
- Focused sequences percent – Minimal percent of sequences in yes-set which actually contains sites of site models in focus
- Sequence column – Column to take sequences from
- Sequences in focus – Selected sequences should be in the result top
- Top sequences size (percent) – Size of sequences (in percent) that will be considered as top
- Sequences in focus in top (percent) – Minimal percent of sequences in focus in the top
- 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
- Pairs mode – Whether the sites of at least two different site models satisfying the cut-off condition must be present on the sequence
- Output path – Path to store result