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

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 <jitao_david.zhang@roche.com>

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")
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(KEGGgraph)

Attaching package: 'KEGGgraph'

The following object is masked from 'package:graphics':

    plot

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGgraph/queryKEGGsubgraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: queryKEGGsubgraph
> ### Title: Query the subgraph of a given KEGG graph with Entrez GeneID (s)
> ### Aliases: queryKEGGsubgraph
> 
> ### ** 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")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

> #}
> 
> ## add missing nodes
> list2 <- c(geneids, 81029)
> sub2 <- queryKEGGsubgraph(list2, gR,addmissing=TRUE)
> #if(require(Rgraphviz) && interactive()) {
>   plot(sub2, "neato")
> #}
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>