R: Tranlate the KEGG graph from being indexed by KEGGID to...
translateKEGGgraph
R Documentation
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
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.
You are welcome to redistribute it under certain conditions.
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/translateKEGGgraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: translateKEGGgraph
> ### Title: Tranlate the KEGG graph from being indexed by KEGGID to another
> ### identifer
> ### Aliases: translateKEGGgraph
>
> ### ** 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
A graphNEL graph with directed edges
Number of Nodes = 4
Number of Edges = 3
> nodes(sub2G)
[1] "DUSP6" "MAPK14" "ELK1" "RPS6KA4"
>
> #if(require(Rgraphviz) & interactive()) {
> plot(sub2G, "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
> #}
>
>
>
>
>
> dev.off()
null device
1
>