shortestPathsGraph: shortestPathsGraph: Construct a subgraph of KEGG global graph...
In azampvd/DrugDiseaseNet: A Systems Biology Approach for Drug Repurposing
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
shortestPathsGraph: Construct a subgraph of KEGG global
graph connecting drug targets and disease-related genes.
Usage
1
shortestPathsGraph(drug_targets, disease_genes, ggraph)
Arguments
drug_targets
the vector of drug target genes
disease_genes
the vector of disease-related genes
ggraph
KEGG global graph as object of type graphNEL
Value
An object of class graphNEL encoding
the a subgraph of KEGG global graph
Author(s)
Azam Peyvandipour and Sorin Draghici
References
Draghici S., et.al.: "A systems biology approach for
pathway level analysis".
Genome Research, 17, 2007.
See Also
Examples
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#obtain KEGG global graph gg
gg<-keggGlobalGraph()
#drug target genes can be obtained from The Comparative
#Toxicogenomics Database (CTD)
drug_targets<-c("hsa:9368","hsa:2322", "hsa:3932", "hsa:4067", "hsa:6714")
#disease-related genes can be obtained from The Comparative
#Toxicogenomics Database (CTD)
disease_genes<-c("hsa:1832" ,"hsa:5073" ,"hsa:5328")
#obtain drug-disease network
mygraph<-shortestPathsGraph(drug_targets,disease_genes,gg)
azampvd/DrugDiseaseNet documentation built on May 7, 2019, 8:58 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
Description
shortestPathsGraph: Construct a subgraph of KEGG global graph connecting drug targets and disease-related genes.
Usage
1 | shortestPathsGraph(drug_targets, disease_genes, ggraph)
|
Arguments
drug_targets |
the vector of drug target genes |
disease_genes |
the vector of disease-related genes |
ggraph |
KEGG global graph as object of type |
Value
An object of class graphNEL encoding
the a subgraph of KEGG global graph
Author(s)
Azam Peyvandipour and Sorin Draghici
References
Draghici S., et.al.: "A systems biology approach for pathway level analysis". Genome Research, 17, 2007.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 | #obtain KEGG global graph gg
gg<-keggGlobalGraph()
#drug target genes can be obtained from The Comparative
#Toxicogenomics Database (CTD)
drug_targets<-c("hsa:9368","hsa:2322", "hsa:3932", "hsa:4067", "hsa:6714")
#disease-related genes can be obtained from The Comparative
#Toxicogenomics Database (CTD)
disease_genes<-c("hsa:1832" ,"hsa:5073" ,"hsa:5328")
#obtain drug-disease network
mygraph<-shortestPathsGraph(drug_targets,disease_genes,gg)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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