inst/hotnet2-example/README.md

In hyginn/rete: Network Analysis for Cell- and Systems Biology

• This is from running with the example files on the hotnet2 homepage. I added the output achieved from running

python makeRequiredPPRFiles.py @example/configs/influence_matrix.config

followed by

python runHotNet2.py @example/configs/simple.config

I also added this readme file and renamed the original readme to README-hotnet2.md.

Output file explanations

The configuration files used to obtain this output can be found under ./config. Note that I included the output from the second Hotnet2 example file, which can be found in the directories appended with a "2".

./influences_matrices{1,2}

• The permuted networks folder holds permutations of the current network structure.
• example_edge_list is the existing edges in the network.
• example_index_genes is the legend for how to map numbers to genes.
• example_ppr_0.6.h5 is the influence matrix.

./output/simple{1,2}/delta_0.{[0-9]*}

• The number in the folder name indicate the threshold used.
• components.txt contains the genes of the significantly altered subnetworks. Genes are tab-separated and subnetworks are listed one per line.
• significance.txt includes the expected and actual number of subnetworks of a specific size, and an associated p-value.
• results.json contains the output from significance.txt under the key statistics, the output from components.txt under the key components, the network size, and the parameter information.
• heat.json contains the heat-values for each gene in the input network.

hyginn/rete documentation built on May 17, 2019, 9:16 p.m.