Download and parse KEGG pathway data

Description

Download and parse KEGG pathway data

Usage

keggPathwayGraphs(organism = "hsa", targRelTypes = c("GErel", "PCrel",
  "PPrel"), relPercThresh = 0.9, nodeOnlyGraphs = FALSE,
  updateCache = FALSE, verbose = TRUE)

Arguments

Value

A list of graphNEL objects encoding the pathway information.

Author(s)

Calin Voichita and Sorin Draghici

See Also

keggPathwayNames

Examples

# The pathway cache provided as part of the pathway contains only the 
# pathways that passed the default filtering. We recommend, re-downloading
# the pathways using the updateCache parameter
kpg <- keggPathwayGraphs("hsa")

# to update the pathway cache for human run:
# kpg <- keggPathwayGraphs("hsa", updateCache = TRUE)
# this is time consuming and depends on the available bandwith.

head(names(kpg))

kpg[["path:hsa04110"]]
head(nodes(kpg[["path:hsa04110"]]))
head(edges(kpg[["path:hsa04110"]]))

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.
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(ROntoTools)
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, 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

Loading required package: boot
Loading required package: KEGGREST
Loading required package: KEGGgraph

Attaching package: 'KEGGgraph'

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

    plot

Loading required package: Rgraphviz
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ROntoTools/keggPathwayGraphs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: keggPathwayGraphs
> ### Title: Download and parse KEGG pathway data
> ### Aliases: keggPathwayGraphs
> 
> ### ** Examples
> 
> 
> # The pathway cache provided as part of the pathway contains only the 
> # pathways that passed the default filtering. We recommend, re-downloading
> # the pathways using the updateCache parameter
> kpg <- keggPathwayGraphs("hsa")
Using cached pathway data. Database info:
pathway          KEGG Pathway Database
path             Release 73.0+/01-03, Jan 15
                 Kanehisa Laboratories
                 343,170 entries
Default parameters detected. Using pre-parsed data.
> 
> # to update the pathway cache for human run:
> # kpg <- keggPathwayGraphs("hsa", updateCache = TRUE)
> # this is time consuming and depends on the available bandwith.
> 
> head(names(kpg))
[1] "path:hsa03008" "path:hsa03013" "path:hsa03015" "path:hsa03018"
[5] "path:hsa03320" "path:hsa03460"
> 
> kpg[["path:hsa04110"]]
A graphNEL graph with directed edges
Number of Nodes = 124 
Number of Edges = 632 
> head(nodes(kpg[["path:hsa04110"]]))
[1] "hsa:1029"  "hsa:51343" "hsa:4171"  "hsa:4172"  "hsa:4173"  "hsa:4174" 
> head(edges(kpg[["path:hsa04110"]]))
$`hsa:1029`
[1] "hsa:4193" "hsa:1019" "hsa:1021" "hsa:595"  "hsa:894"  "hsa:896" 

$`hsa:51343`
[1] "hsa:983"   "hsa:85417" "hsa:891"   "hsa:9133" 

$`hsa:4171`
character(0)

$`hsa:4172`
character(0)

$`hsa:4173`
character(0)

$`hsa:4174`
character(0)

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>