Obtain KEGG pathway titles

Description

Obtain KEGG pathway titles

Usage

keggPathwayNames(organism = "hsa", updateCache = FALSE, verbose = TRUE)

Arguments

Value

A named vector of pathway titles. The names of the vector are the pathway KEGG IDs.

Author(s)

Calin Voichita and Sorin Draghici

See Also

keggPathwayGraphs

Examples

kpn <- keggPathwayNames("hsa")

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

head(kpn)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/keggPathwayNames.Rd_%03d_medium.png", width=480, height=480)
> ### Name: keggPathwayNames
> ### Title: Obtain KEGG pathway titles
> ### Aliases: keggPathwayNames
> 
> ### ** Examples
> 
> 
> kpn <- keggPathwayNames("hsa")
Using cached pathway data. Database info:
pathway          KEGG Pathway Database
path             Release 73.0+/01-03, Jan 15
                 Kanehisa Laboratories
                 343,170 entries
> 
> # to update the pathway cache for human run:
> # kpn <- keggPathwayNames("hsa", updateCache = TRUE)
> # this is time consuming and depends on the available bandwidth.
> 
> head(kpn)
                      path:hsa03008                       path:hsa03013 
"Ribosome biogenesis in eukaryotes"                     "RNA transport" 
                      path:hsa03015                       path:hsa03018 
        "mRNA surveillance pathway"                   "RNA degradation" 
                      path:hsa03320                       path:hsa03460 
           "PPAR signaling pathway"            "Fanconi anemia pathway" 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>