translateKEGGgraph: Tranlate the KEGG graph from being indexed by KEGGID to...

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

Tranlate the KEGG graph from being indexed by KEGGID to another identifer

Description

The function translates the KEGG graph into a graph of equivalant topology while index with unique identifiers given by user. The new identifiers could be, for example, GeneSymbol or other identifiers mapped to KEGGID.

Usage

translateKEGGgraph(graph, newNodes)

Arguments

graph	A KEGG graph
newNodes	A character vector giving the new nodes, must be of the same length and same order of the nodes of the given graph

Details

The function is still experimental and users are welcomed to report any difficulties

Value

Another graph indexed by the given identifier

Author(s)

Jitao David Zhang <[e-mail]>

Examples

sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
gR <- parseKGML2Graph(sfile,expandGenes=TRUE)

subG <- subKEGGgraph(c("hsa:1848","hsa:1432","hsa:2002","hsa:8986"),gR)
symbols <- c("DUSP6","MAPK14","ELK1","RPS6KA4")
sub2G <- translateKEGGgraph(subG, symbols)
sub2G
nodes(sub2G)

if(require(Rgraphviz) & interactive()) {
plot(sub2G, "neato")
}

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