downloadPathways: Download KEGG pathways in KGML format.

In CHRONOS: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

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)

CHRONOS documentation built on Nov. 8, 2020, 8:30 p.m.