18 Output network
A network may be output using the -output-network task. The network may be output in one of three different formats. The -output-network-igraph-file-prefix option can also be used to output igraph files, see section 21 for more details.
The output network task can also be used to output node data using the -output-network-node-data-file-prefix option and optionally the -output-network-node-data-bed-file option.
The options are as follows:
| Option | Description | Default |
|---|
| -output-network | do a task to output a network to file | |
| -output-network-name name | label the task with a name | Task-n |
| -output-network-network-name network | output this network | previous network (or the default model given by a node for each data variable and no edges if there is no previous network) |
| -output-network-file network.dat | output the network in a format where the nodes and then the edges are listed | |
| -output-network-file2 network2.dat | output the network in this style of format: [a][b|a][c|a:b] | |
| -output-network-equivalent-networks-file equiv-networks.dat | output a list of equivalent networks to file equiv-networks.dat | |
| -output-network-igraph-file-prefix mygraph | output igraph format files consisting of mygraph-nodes.dat, mygraph-edges.dat and R code mygraph-plot.R | |
| -output-network-node-data-file-prefix mydata | output network discrete data to mydata-discrete.dat and continuous data to mydata-cts.dat | |
| -output-network-node-data-bed-file | output SNP data to files mydata.bed, mydata.bim and mydata.fam and not to files mydata-discrete.dat and mydata-cts.dat | |
| -output-network-node-data-start-indiv a | start output of data from individual a | 1 |
| -output-network-node-data-end-indiv b | stop output of data at individual b | last individual |
| -output-network-node-data-job i t | only output individuals for subset i from a total of t subsets | |
The following is an example parameter file to output a network.
#input continuous data
-input-data
-input-data-file example-cts.dat
-input-data-cts
#input discrete data
-input-data
-input-data-file example-discrete.dat
-input-data-discrete
#input SNP data as discrete data
-input-data
-input-data-file example.bed
-input-data-discrete-snp
#search network models
-search-models
#output the fitted network
-output-network
-output-network-file fittedNetwork.dat
This parameter file, paras-output-network.txt, can be found in example.zip and can be used as follows:
./bayesnetty paras-output-network.txt
Which should produce output that looks like something as follows:
BayesNetty: Bayesian Network software, v1.00
--------------------------------------------------
Copyright 2015-present Richard Howey, GNU General Public License, v3
Institute of Genetic Medicine, Newcastle University
Random seed: 1551716789
--------------------------------------------------
Task name: Task-1
Loading data
Continuous data file: example-cts.dat
Number of ID columns: 2
Including (all) 2 variables in analysis
Each variable has 1500 data entries
Missing value: not set
--------------------------------------------------
--------------------------------------------------
Task name: Task-2
Loading data
Discrete data file: example-discrete.dat
Number of ID columns: 2
Including the 1 and only variable in analysis
Each variable has 1500 data entries
Missing value: NA
--------------------------------------------------
--------------------------------------------------
Task name: Task-3
Loading data
SNP binary data file: example.bed
SNP data treated as discrete data
Total number of SNPs: 2
Total number of subjects: 1500
Number of ID columns: 2
Including (all) 2 variables in analysis
Each variable has 1500 data entries
--------------------------------------------------
--------------------------------------------------
Task name: Task-4
Searching network models
--------------------------------------------------
Loading defaultNetwork network
Network type: bnlearn
Network score type: BIC
Total number of nodes: 5 (Discrete: 3 | Factor: 0 | Continuous: 2)
Total number of edges: 0
Network Structure: [express][pheno][mood][rs1][rs2]
Total data at each node: 1495
Missing data at each node: 5
--------------------------------------------------
Network: defaultNetwork
Search: Greedy
Random restarts: 0
Random jitter restarts: 0
Network Structure: [mood][rs1][rs2][express|rs1:rs2][pheno|express:mood]
Network score type: BIC
Network score = -8213.45
--------------------------------------------------
--------------------------------------------------
Task name: Task-5
Outputting network
Network: defaultNetwork
Network Structure: [mood][rs1][rs2][express|rs1:rs2][pheno|express:mood]
Network output to file: fittedNetwork.dat
--------------------------------------------------
Run time: less than one second
The data is loaded, a search is performed and then the network is output to a file.
