kegg_pathways: List of KEGG signaling pathways of human.

In mirIntegrator: Integrating microRNA expression into signaling pathways for pathway analysis

Description

This dataset contains 149 KEGG signaling pathways of human. The original pathways were parsed to a list of graphNEL objects using the ROntoTools package. The original KEGG pathways were published by Kanehisa Laboratories, release 73.0+/01-03, Jan 2015.

Usage

data("kegg_pathways")

Value

A list of graphNEL objects where each graph represents one KEGG signaling pathway. The name of each pathway is its KEGG pathway identifier.

Source

Obtained using the ROntoTools package Version 1.2.0 with KEGG database release 73.0+/01-03, Jan 2015. A script that constructs the kegg_pathways object may be found in 'inst/scripts/get_kegg_pathways.R', see the example.

References

M. Kanehisa and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol. 28, pp. 27-30, January 2000.

C. Voichita, M. Donato, and S. Draghici, Incorporating gene significance in the impact analysis of signaling pathways, in 2012 11th International Conference on Machine Learning and Applications (ICMLA), vol. 1, pp. 126-131, Dec. 2012.

Examples

data(kegg_pathways)
head(kegg_pathways)

script <- system.file("scripts", "get_kegg_pathways.R", 
                      package = "mirIntegrator")
script
readLines(script)

Example output

$`path:hsa03008`
A graphNEL graph with directed edges
Number of Nodes = 84 
Number of Edges = 2 

$`path:hsa03013`
A graphNEL graph with directed edges
Number of Nodes = 165 
Number of Edges = 265 

$`path:hsa03015`
A graphNEL graph with directed edges
Number of Nodes = 91 
Number of Edges = 156 

$`path:hsa03018`
A graphNEL graph with directed edges
Number of Nodes = 77 
Number of Edges = 73 

$`path:hsa03320`
A graphNEL graph with directed edges
Number of Nodes = 69 
Number of Edges = 251 

$`path:hsa03460`
A graphNEL graph with directed edges
Number of Nodes = 53 
Number of Edges = 80 

[1] "/usr/lib/R/site-library/mirIntegrator/scripts/get_kegg_pathways.R"
 [1] "# The following script downloads the kegg_pathways dataset"
 [2] "# included in the mirIntegrator package. "                 
 [3] "# This dataset is included only for demostration purposes."
 [4] ""                                                          
 [5] "library(\"ROntoTools\")"                                   
 [6] "kegg_pathways_O <- keggPathwayGraphs(\"hsa\")"             
 [7] ""                                                          
 [8] "set.gene.id <- function(pathway.i)"                        
 [9] "{"                                                         
[10] "  genes.i <- nodes(pathway.i)"                             
[11] "  ent.gen.i <- gsub(\".*\\\\:\",\"\",genes.i)"             
[12] "  nodes(pathway.i) <- ent.gen.i"                           
[13] "  pathway.i"                                               
[14] "}"                                                         
[15] ""                                                          
[16] "kegg_pathways <- lapply(kegg_pathways_O, set.gene.id)"     
[17] ""                                                          
[18] "save(kegg_pathways, file = \"kegg_pathways.rda\")"         
[19] "library(tools)"                                            
[20] "resaveRdaFiles(\"kegg_pathways.rda\")"                     

mirIntegrator documentation built on Nov. 8, 2020, 8:28 p.m.