Converts Bioplanet pathways from (https://tripod.nih.gov/bioplanet/) into a list of pathways whose elements are the genes in each pathway. Edge weights are either the PTM Cluster Weight or according to the Jaccard Similarity.
Arguments
- common.clusters
The list of common clusters between all three distance metrics (Euclidean, Spearman, and SED). Can be made in MakeCorrelationNetwork
- bioplanet.file
Either the path to a delimited Bioplanet file, or a named list of pathways where each list element is a character vector of gene symbols.
Value
A list with these data structures at the given index:
Contains pathway source-target columns, along with the interaction type.
Contains pathway source-target columns, with edge weights of their jaccard similarity and their Pathway-Pathway Evidence score.
All pathways in the bioplanet database as a named list containing string vectors. Each vector is a pathway with strings associated with the genes in that pathway.
The cluster-by-pathway CPE matrix used to compute PTM cluster weights.
Examples
Example_Output <- BuildPathwayCrosstalkNetwork(ex_common_clusters, ex_pathways_list)
#> Making PCN
#> 2026-06-30 17:52:28.551926
#> 2026-06-30 17:52:28.657752
#> Total time: 0.105825424194336
head(Example_Output[[1]])
#> source
#> 4 Axon guidance
#> 2 Axon guidance
#> 3 Axon guidance
#> 5 ERBB signaling pathway
#> 18 Selenium pathway
#> 10 Lipid and lipoprotein metabolism
#> target Weight
#> 4 Validated nuclear estrogen receptor alpha network 1.27898550724638
#> 2 ERBB signaling pathway 9.50912807669002
#> 3 Lipid and lipoprotein metabolism 4.63387820142684
#> 5 Lipid and lipoprotein metabolism 2.96007824348337
#> 18 Vitamin B12 metabolism 0.866666666666667
#> 10 Selenium pathway 0.3
#> interaction
#> 4 PTM_cluster_weights
#> 2 PTM_cluster_weights
#> 3 PTM_cluster_weights
#> 5 PTM_cluster_weights
#> 18 PTM_cluster_weights
#> 10 PTM_cluster_weights