An annotation data object that maps Entrez Gene or Open Reading Frame identifiers KEGG pathway identifiers

Description

KEGGEXTID2PATHID maps Entrez Gene (for human, mouse, and rat) and Open Reading Frame (for yeast) identifiers to KEGG pathway identifiers.

Details

This is an R object containing key and value pairs. Keys are Entrez Gene identifiers for human, mouse, and rat and Open Reading Frame (ORF) identifiers for yeast and values are the corresponding KEGG pathway identifiers. Values are vectors of length 1 or greater depending on whether a given external identifier can be mapped to only one or more KEGG pathway identifiers. NAs are assigned to Entrez Gene or ORF identifiers that can not be mapped to any pathway identifier.

KEGG pathway identifiers are the identifiers used by KEGG for various pathways.

Mappings between KEGG pathway identifiers and pathway names can be obtained through another annotation data object named KEGGPATHID2NAME.

Mappings were based on data provided by: KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15

References

ftp://ftp.genome.ad.jp/pub/kegg/pathways

See Also

• AnnotationDb-class for use of the select() interface.

Examples

## select() interface:
## Objects in this package can be accessed using the select() interface
## from the AnnotationDbi package. See ?select for details.

## Bimap interface:
xx <- as.list(KEGGEXTID2PATHID)
if(length(xx) > 0){
    # Get the value of the first key
    xx[[1]]
    # Get the values for multiget for a few keys
    if(length(xx) >= 3){
    	xx[1:3]
    }
}

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(KEGG.db)
Loading required package: AnnotationDbi
Loading required package: stats4
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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGG.db/KEGGEXTID2PATHID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KEGGEXTID2PATHID
> ### Title: An annotation data object that maps Entrez Gene or Open Reading
> ###   Frame identifiers KEGG pathway identifiers
> ### Aliases: KEGGEXTID2PATHID
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## select() interface:
> ## Objects in this package can be accessed using the select() interface
> ## from the AnnotationDbi package. See ?select for details.
> 
> ## Bimap interface:
> xx <- as.list(KEGGEXTID2PATHID)
> if(length(xx) > 0){
+     # Get the value of the first key
+     xx[[1]]
+     # Get the values for multiget for a few keys
+     if(length(xx) >= 3){
+     	xx[1:3]
+     }
+ }
$`10`
[1] "hsa00232" "hsa00983" "hsa01100"

$`100`
[1] "hsa00230" "hsa01100" "hsa05340"

$`1000`
[1] "hsa04514" "hsa05412"

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