queryKEGGsubgraph {KEGGgraph} | R Documentation

## Query the subgraph of a given KEGG graph with Entrez GeneID (s)

### Description

Given a list of genes (identified by Entrez GeneID), the function subsets the given KEGG gragh of the genes as nodes (and maintaining all the edges between).

### Usage

    queryKEGGsubgraph(geneids, graph, organism = "hsa", addmissing = FALSE)

### Arguments

`geneids` | A vector of Entrez GeneIDs
`graph` | A KEGG graph
`organism` | a three-alphabet code of organism
`addmissing` | logical, in case the given gene is not found in the graph, should it be added as single node to the subgraph?

### Details

This function solves the questions like 'How is the list of gene interact with each other in the context of pathways?'

Limited by the `translateKEGGID2GeneID`, this function supports only human for now. We are working to include other organisms.

If 'addmissing' is set to `TRUE`, the missing gene in the given list will be added to the returned subgraph as single nodes.

### Value

A subgraph with nodes representing genes and edges representing interactions.

### Author(s)

Jitao David Zhang <j.zhang@dkfz.de>

### See Also

`translateGeneID2KEGGID`

### Examples

    sfile <- system.file("extdata/hsa04010.xml",package="KEGGgraph")
    gR <- parseKGML2Graph(sfile,expandGenes=TRUE)
    geneids <- c(5594, 5595, 6197, 5603, 1843,5530, 5603)
    sub <- queryKEGGsubgraph(geneids, gR)
    if(require(Rgraphviz) && interactive()) {
      plot(sub, "neato")
    }

    ## add missing nodes
    list2 <- c(geneids, 81029)
    sub2 <- queryKEGGsubgraph(list2, gR,addmissing=TRUE)
    if(require(Rgraphviz) && interactive()) {
      plot(sub2, "neato")
    }

[Package KEGGgraph version 1.1.0 Index]