retrieve_topology.RdRetrieve pathway topology matrices and convert to normalized weighted directed adjacency matrices describing gene signaling networks.
retrieve_topology(database, pathwayName = NULL, beta = NULL, outputDir)See example for supported databases.
Optional. Subset of pathway names as a vector.
Optional. A named numeric vector of weights to be assigned to each type of gene/protein relation type. See details for more information.
A file directory specifying where the weighted adjacent matrix should be stored as an RData object.
A list where each element is a matrix corresponding to a pathway
This function takes the pathway topology information retrieved using graphite and convert them to normalized weighted directed adjacency
matrices describing the gene signaling network, which can be directed used to compute pathway perturbation score through SPIA algorithm.
See cited document for more details.
The beta parameter specifies weights to be assigned to each type of gene-gene interaction. It should be a named numeric vector of length 23, whose names must be: c("activation","compound","binding/association","expression","inhibition","activation_phosphorylation","phosphorylation", "indirect","inhibition_phosphorylation","dephosphorylation_inhibition","dissociation","dephosphorylation","activation_dephosphorylation", "state","activation_indirect","inhibition_ubiquination","ubiquination","expression_indirect","indirect_inhibition", "repression","binding/association_phosphorylation","dissociation_phosphorylation","indirect_phosphorylation"). If unspecified, beta will be by default chosen as: c(1,0,0,1,-1,1,0,0,-1,-1,0,0,1,0,1,-1,0,1,-1,-1,0,0,0).
The converted weighted adjacent matrices will be stored in list and write into the file directory specified through the outputDir parameter.
This function only supports and can only be used to retreive human databases as this stage.
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R. A novel signaling pathway impact analysis. Bioinformatics. 2009 Jan 1;25(1):75-82. Sales, G., Calura, E., Cavalieri, D. et al. graphite - a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics 13, 20 (2012).
# explore all databases supported by graphite
if (FALSE) {
graphite::pathwayDatabases()
retrieve_topology(database = "kegg",
outputDir = "gsTopology.rda")
}
# if only interested in selected pathways, specify the pathway names in the `pathwayName` parameter
if (FALSE) {
retrieve_topology(database = "kegg",
pathwayName = c("Glycolysis / Gluconeogenesis",
"Citrate cycle (TCA cycle)","Pentose phosphate pathway"),
outputDir = "gsTopology.rda")
}