Map between Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway identifiers and TAIR Identifiers

Description

org.At.tairPATH2TAIR is an R object that provides mappings between KEGG identifiers and TAIR identifiers.

Details

Each KEGG identifier is mapped to a named vector of manufacturer identifiers. The name represents the KEGG identifier and the vector contains all TAIR identifiers that are found in that particular pathway. An NA is reported for any KEGG identifier that cannot be mapped to any TAIR identifiers.

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 http://www.genome.ad.jp/kegg/pathway.html 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:
# Convert the object to a list
xx <- as.list(org.At.tairPATH2TAIR)
# Remove pathway identifiers that do not map to any tair id
xx <- xx[!is.na(xx)]
if(length(xx) > 0){
    # The tair identifiers for the first two elements of XX
    xx[1:2]
    # Get the first one
    xx[[1]]
} 

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(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.tairPATH2TAIR.Rd_%03d_medium.png", width=480, height=480)
> ### Name: org.At.tairPATH2TAIR
> ### Title: Map between Kyoto Encyclopedia of Genes and Genomes (KEGG)
> ###   pathway identifiers and TAIR Identifiers
> ### Aliases: org.At.tairPATH2TAIR
> ### 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:
> # Convert the object to a list
> xx <- as.list(org.At.tairPATH2TAIR)
> # Remove pathway identifiers that do not map to any tair id
> xx <- xx[!is.na(xx)]
> if(length(xx) > 0){
+     # The tair identifiers for the first two elements of XX
+     xx[1:2]
+     # Get the first one
+     xx[[1]]
+ } 
  [1] "AT1G01050" "AT1G02410" "AT1G04630" "AT1G12840" "AT1G15120" "AT1G15690"
  [7] "AT1G15700" "AT1G16700" "AT1G16780" "AT1G17260" "AT1G19910" "AT1G20260"
 [13] "AT1G22450" "AT1G32710" "AT1G49140" "AT1G51650" "AT1G53030" "AT1G64200"
 [19] "AT1G65290" "AT1G75630" "AT1G76030" "AT1G78900" "AT1G79010" "AT1G80230"
 [25] "AT1G80660" "AT2G01090" "AT2G02050" "AT2G07560" "AT2G07671" "AT2G07687"
 [31] "AT2G07698" "AT2G07707" "AT2G07727" "AT2G07741" "AT2G07751" "AT2G07785"
 [37] "AT2G16510" "AT2G18230" "AT2G18450" "AT2G18960" "AT2G19680" "AT2G20360"
 [43] "AT2G20800" "AT2G21410" "AT2G24520" "AT2G25610" "AT2G28520" "AT2G29990"
 [49] "AT2G33040" "AT2G33220" "AT2G44520" "AT2G44620" "AT2G46860" "AT2G47690"
 [55] "AT3G01390" "AT3G03070" "AT3G03100" "AT3G06310" "AT3G08560" "AT3G08610"
 [61] "AT3G12260" "AT3G15352" "AT3G15640" "AT3G18410" "AT3G27240" "AT3G27380"
 [67] "AT3G28710" "AT3G28715" "AT3G42050" "AT3G42640" "AT3G47950" "AT3G52300"
 [73] "AT3G52730" "AT3G53620" "AT3G58730" "AT3G60330" "AT3G62790" "AT4G01480"
 [79] "AT4G02580" "AT4G02620" "AT4G04640" "AT4G05020" "AT4G09650" "AT4G11150"
 [85] "AT4G21490" "AT4G23710" "AT4G25950" "AT4G26210" "AT4G26710" "AT4G28060"
 [91] "AT4G28220" "AT4G29480" "AT4G30190" "AT4G32260" "AT4G32470" "AT4G32530"
 [97] "AT4G34700" "AT4G34720" "AT4G37830" "AT4G38510" "AT4G38920" "AT4G39080"
[103] "AT5G08530" "AT5G08670" "AT5G08680" "AT5G08690" "AT5G09650" "AT5G11770"
[109] "AT5G13430" "AT5G13440" "AT5G13450" "AT5G18800" "AT5G25450" "AT5G37510"
[115] "AT5G40650" "AT5G40810" "AT5G47030" "AT5G47890" "AT5G52840" "AT5G55290"
[121] "AT5G56090" "AT5G57350" "AT5G57815" "AT5G62670" "AT5G65165" "AT5G66760"
[127] "AT5G67590"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>