https://github.com/mllg/stability-bioinf
Supplementary Scripts and Data
https://github.com/mllg/stability-bioinf
Last synced: about 1 month ago
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Supplementary Scripts and Data
- Host: GitHub
- URL: https://github.com/mllg/stability-bioinf
- Owner: mllg
- License: mit
- Created: 2016-12-20T13:56:58.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2017-06-07T12:46:28.000Z (almost 8 years ago)
- Last Synced: 2025-03-31T15:25:50.944Z (about 1 month ago)
- Language: R
- Size: 17.3 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Description of the content of this repository
All R files must be executed with working directory set to the place they are stored.
The experiments were run on a parallel computer system and create intermediate files used in the later analysis.
If you want to avoid re-computation, we are happy to provide our computations upon request via email (the result files consume several GB and are therefore not hosted here).
## Overview of the workflow:
1. Creation and description of the data sets (see folder Data)
2. Conduction of experiments (see folders Experiments)
3. Evaluation of the experiments (see folders Evaluation)
## Data:
- data sets used for the analysis
- data_preprocessing.R: creation of the three data sets as *.RData files
- data_properties: PCA plots used for displaying the properties of the data
## Measures comparison:
### Experiments:
- measures_comparison_experiments.R: experiments for the empirical comparison of the stability measures
- measures_comparison_results.R: collection of the results of the experiments for the empirical comparison of the stability measures
### Evaluation:
- evaluation of the experiments of the empirical comparison of the stability measures
- measures_comparison_evaluation.R: main file for the evaluation of the experiments
- ggplot_functions.R: contains plotting functions
- pareto_optimal.R: selects Pareto optimal models for each data set
## Model finding:
### Experiments:
- model_finding_experiments.R: experiments for the random search for desirable configurations
- model_finding_results.R: collection of the results of the experiments for the random search for desirable configurations
### Evalutaion:
- evaluation of the experiments of the random search for desirable configurations
- model_finding_evaluation.R: main file for the evaluation of the experiments