queryKEGGsubgraph: Query the subgraph of a given KEGG graph with Entrez GeneID...

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

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 <[e-mail]>

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")
}

Example output

Attaching package: 'KEGGgraph'

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

    plot

Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: grid

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.