downloadPathways {CHRONOS} | R Documentation

## Download KEGG pathways in KGML format.

### Description

Download KEGG pathways in KGML format.

### Usage

    downloadPathways(org, pathways)

### Arguments

`org` | KEGG organism identifier
`pathways` | Download pathways for specified organism:
| 'All' | All organism pathways
| 'Metabolic' | Metabolic pathways
| 'Non-Metabolic' | Non metabolic pathways
| <vector of indexes> | Using indexes from `downloadKEGGPathwayList`
| <vector of names> | Using pathway identifiers (i.e. c('00010', '00020'))

### Details

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database resource for understanding high-level functions and utilities of the biological , system such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

Files are downloaded in CHRONOS/extdata/Downloads/KEGG/<org> folder.
Downloading is skipped for existing files.

### Value

Downloaded data is stored in CHRONOS/extdata/Downloads/KEGG/<org>

### References

- http://www.genome.jp/kegg/pathway.html

### Examples

    # View all availiable hsa pathways
    ## Not run: pathways <- downloadKEGGPathwayList(org='hsa')

    # Download pathway KGML files
    pathways <- c('04915', '04917', '04930', '05031')

    ## Not run: pathways <- downloadPathways(org='hsa', pathways=pathways)

[Package CHRONOS version 1.10.1 Index]