panev.pathList: PANEV pathways codes

In vpalombo/PANEV: PaNeV: an R package for a pathway-based network visualization

PANEV pathways codes

Description

The function retrieves the list of the available pathways in KEGG, according to a user defined search string. If path = NULL the list of all available pathways is returned. To run all core PANEV functions a list of pathways of interest, coded with KEGG 'path_ID', is required.

Usage

panev.pathList(string = NULL)

Arguments

string

A string used to search within the description field of all KEGG available pathways (default = NULL).

Details

This function is based on the keggList function of KEGGREST package (http://bioconductor.org/packages/release/bioc/html/KEGGREST.html.

Value

A dataframe containing two columns with KEGG path description and path ID respectively.

Author(s)

Valentino Palombo ([e-mail])

References

Tenenbaum D (2017). KEGGREST: Client-side REST access to KEGG. R package version 1.16.1.

Examples

##### EXAMPLES CODE #####
#Create a list of all available pathways for PANEV
list <- panev.pathList(string = NULL)

#Look for a specific pathway(s) in PANEV, matching your search string
list <- panev.pathList(string = "lipid")

vpalombo/PANEV documentation built on June 13, 2022, 1:11 p.m.