MS_getPathIds {MetaboSignal} | R Documentation

## Get pathway identifiers of a given organism

### Description

This function retrieves the identifiers (IDs) of all metabolic and signaling KEGG pathways of a given organism. These pathway IDs can be used to build a MetaboSignal network with the function "MS_keggNetwork( )".

### Usage

    MS_getPathIds(organism_code)

### Arguments

`organism_code` | character vector containing the KEGG code for the organism of interest. For example the KEGG code for the rat is "rno". See the function "MS_keggFinder( )".

### Value

This function returns a matrix, where each row contains the ID, description, category, and type (i.e. "metabolic" or "signaling") of each pathway. This matrix is also exported in a file named "organism-code_pathways.txt".

### References

Tenenbaum, D. KEGGREST: Client-side REST access to KEGG. R package version >= 1.17.0.

### Examples

    rat_paths <- MS_getPathIds(organism_code = "rno")
    human_paths <- MS_getPathIds(organism_code = "hsa")

[Package MetaboSignal version 1.12.0 Index]