List of KEGG signaling pathways' names.

Description

Names of the KEGG signaling pathways in human obtained with the ROntoTools package. The original KEGG pathways were published by Kanehisa Laboratories, release 73.0+/01-03, Jan 2015.

Usage

data("names_pathways")

Value

A list of KEGG signaling pathways' names.

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 names_pathways object may be found in 'inst/scripts/get_names_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(names_pathways)
 head(names_pathways)
 
 script <- system.file("scripts", "get_names_pathways.R", 
                      package = "mirIntegrator")
 script
 readLines(script)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mirIntegrator)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirIntegrator/names_pathways.Rd_%03d_medium.png", width=480, height=480)
> ### Name: names_pathways
> ### Title: List of KEGG signaling pathways' names.
> ### Aliases: names_pathways
> ### Keywords: datasets
> 
> ### ** Examples
> 
>  data(names_pathways)
>  head(names_pathways)
                      path:hsa03008                       path:hsa03013 
"Ribosome biogenesis in eukaryotes"                     "RNA transport" 
                      path:hsa03015                       path:hsa03018 
        "mRNA surveillance pathway"                   "RNA degradation" 
                      path:hsa03320                       path:hsa03460 
           "PPAR signaling pathway"            "Fanconi anemia pathway" 
>  
>  script <- system.file("scripts", "get_names_pathways.R", 
+                       package = "mirIntegrator")
>  script
[1] "/home/ddbj/local/lib64/R/library/mirIntegrator/scripts/get_names_pathways.R"
>  readLines(script)
 [1] "# The following script downloads the names_pathways list"
 [2] "# included in the mirIntegrator package. "               
 [3] "# This list is included only for demostration purposes." 
 [4] ""                                                        
 [5] "library("ROntoTools")"                                 
 [6] "names_pathways <- keggPathwayNames("hsa")"             
 [7] "save(names_pathways, file = "names_pathways.rda")"     
 [8] "library(tools)"                                          
 [9] "resaveRdaFiles("names_pathways.rda")"                  
[10] ""                                                        
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>