Mappings between TAIR identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. org.At.tairPATH maps TAIR identifiers to the identifiers used by KEGG for pathways in which the genes represented by the TAIR identifiers are involved

Details

Each KEGG pathway has a name and identifier. Pathway name for a given pathway identifier can be obtained using the KEGG data package that can either be built using AnnBuilder or downloaded from Bioconductor http://www.bioconductor.org.

Graphic presentations of pathways are searchable at url http://www.genome.ad.jp/kegg/pathway.html by using pathway identifiers as keys.

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

http://www.genome.ad.jp/kegg/

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:
x <- org.At.tairPATH
# Get the TAIR identifiers that are mapped to a KEGG pathway ID
mapped_genes <- mappedkeys(x)
# Convert to a list
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
  # Get the PATH for the first five genes
  xx[1:5]
  # Get the first one
  xx[[1]]
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(org.At.tair.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


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/org.At.tair.db/org.At.tairPATH.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.At.tairPATH
> ### Title: Mappings between TAIR identifiers and KEGG pathway identifiers
> ### Aliases: org.At.tairPATH
> ### 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:
> x <- org.At.tairPATH
> # Get the TAIR identifiers that are mapped to a KEGG pathway ID
> mapped_genes <- mappedkeys(x)
> # Convert to a list
> xx <- as.list(x[mapped_genes])
> if(length(xx) > 0) {
+   # Get the PATH for the first five genes
+   xx[1:5]
+   # Get the first one
+   xx[[1]]
+ }
[1] "00190"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>