BayesNetty: Bayesian Network Software for Genetic Analyses

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1 Introduction
2 Installation
3 Using BayesNetty
- 3.1 Basic Options
- 3.2 Parameter file
- 3.3 Simple Example
- 3.4 Command-line Options
4 Parallel BayesNetty
- 4.1 Compilation Scripts
5 Input data
- 5.1 Options
- 5.2 Discrete data
- 5.3 Continuous data
- 5.4 Factor data
- 5.5 SNP data
- 5.6 Missing data
- 5.7 Data IDs
- 5.8 Example
6 Input network
- 6.1 Options
- 6.2 Black lists
- 6.3 White lists
- 6.4 Soft Constraints
- 6.5 Network formats
- 6.6 Example
7 bnlearn network
- 7.1 Network score
8 deal network
- 8.1 Imaginary sample size
9 Calculate network score
- 9.1 Options
- 9.2 Example
10 Calculate posterior
- 10.1 Options
- 10.2 Example
11 Search models
- 11.1 Options
- 11.2 Greedy search
- 11.3 Example
12 Average network
- 12.1 Options
- 12.2 Score Method
- 12.3 Example
- 12.4 Parallel Example
13 Impute Data
- 13.1 Options
- 13.2 Example
- 13.3 Parallel Example
14 Estimate Imputation Benefit
- 14.1 Options
- 14.2 Example
15 Calculate Recall and Precision
- 15.1 Options
- 15.2 Example
16 Simulate network data
- 16.1 Options
- 16.2 Example 1: no data
- 16.3 Example 2: data and fitted network
- 16.4 Example 3: data and unknown network
17 Markov blanket
- 17.1 Options
- 17.2 Example
18 Output network
- 18.1 Options
- 18.2 Example
19 Output priors (deal only)
- 19.1 Options
- 19.2 Example
20 Output posteriors
- 20.1 Options
- 20.2 Example
21 Network plotting
- 21.1 igraph
- 21.2 Example
References

Contact

Please contact Richard Howey with any queries about the BayesNetty software.

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