parseKGMLexpandMaps: A convenient function to parse KGML and expand its containing...

In Accio/KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

A convenient function to parse KGML and expand its containing maps into one graph object

Description

The function does several tasks implemented in the KEGGgraph package in sequence to make expanding maps easier.

Usage

parseKGMLexpandMaps(file, downloadmethod = "auto", genesOnly = TRUE, localdir,...)

Arguments

file	A KGML file
downloadmethod	passed to download.file function as 'method', see its documentation for more details
genesOnly	logical, should only the genes nodes remain in the returned graph object?
localdir	character string, if specified, the function tries to read files with the same base name from a local directory, useful when there are file copies on the client.
...	Other parameters passed to download.file

Details

In KEGG pathways there're usually pathways contained('cross-linked') in other pathways, for example see https://www.genome.jp/kegg/pathway/hsa/hsa04115.html, where p53 signalling pathway contains other two pathways 'apoptosis' and 'cell cycle'. This function parses these pathways (refered as 'maps' in KGML manual), download their KGML files from KEGG REST API, parse them individually, and merge all the children pathway graphs with the parental pathway into one graph object. The graph is returned as the function value.

Since different graphs does not have unique node identifiers unless the genes are expanded, so by using this function user has to expand the genes. Another disadvantage is that so far due to the implementation, the KEGGnodeData and KEGGedgeData is lost during the merging. This however will probably be changed in the future version.

Value

A directed graph object

Author(s)

Jitao David Zhang [e-mail]

References

KGML Document manual https://www.genome.jp/kegg/docs/xml/

See Also

for most users it is enough to use parseKGML2Graph

Accio/KEGGgraph documentation built on Jan. 13, 2023, 1:03 p.m.