Mappings between probe identifiers and KEGG pathway identifiers

Description

KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms.

illuminaMousev1PATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved

illuminaMousev1PATH2PROBE is an R object that provides mappings between KEGG identifiers and manufacturer identifiers.

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/

Examples

    x <- illuminaMousev1PATH
    # Get the probe identifiers that are mapped to a KEGG pathway ID
    mapped_probes <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_probes])
    if(length(xx) > 0) {
      # Get the PATH for the first five probes
      xx[1:5]
      # Get the first one
      xx[[1]]
    }

    # Now convert the illuminaMousev1PATH2PROBE object to a list
    xx <- as.list(illuminaMousev1PATH2PROBE)
    if(length(xx) > 0){
        # Get the probe identifiers for the first two pathway identifiers
        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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(illuminaMousev1.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

Loading required package: org.Mm.eg.db


> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/illuminaMousev1.db/illuminaMousev1PATH.Rd_%03d_medium.png", width=480, height=480)
> ### Name: illuminaMousev1PATH
> ### Title: Mappings between probe identifiers and KEGG pathway identifiers
> ### Aliases: illuminaMousev1PATH illuminaMousev1PATH2PROBE
> ### Keywords: datasets
> 
> ### ** Examples
> 
>     x <- illuminaMousev1PATH
>     # Get the probe identifiers that are mapped to a KEGG pathway ID
>     mapped_probes <- mappedkeys(x)
>     # Convert to a list
>     xx <- as.list(x[mapped_probes])
>     if(length(xx) > 0) {
+       # Get the PATH for the first five probes
+       xx[1:5]
+       # Get the first one
+       xx[[1]]
+     }
[1] "04110" "04115" "05200" "05212" "05214" "05218" "05219" "05220" "05223"
> 
>     # Now convert the illuminaMousev1PATH2PROBE object to a list
>     xx <- as.list(illuminaMousev1PATH2PROBE)
>     if(length(xx) > 0){
+         # Get the probe identifiers for the first two pathway identifiers
+         xx[1:2]
+         # Get the first one
+         xx[[1]]
+     } 
 [1] "scl40703.5.1_48-S"   "scl011668.12_94-S"   "scl26088.14.1_16-S" 
 [4] "scl40135.12_123-S"   "scl000942.1_27-S"    "scl17939.35.1_294-S"
 [7] "scl18935.13_58-S"    "scl36896.8.1_213-S"  "scl35783.6.1_22-S"  
[10] "scl0013078.2_259-S"  "scl0013195.2_156-S"  "scl40512.21.1_20-S" 
[13] "scl015107.1_301-S"   "scl21503.2.1_16-S"   "scl015930.1_97-S"   
[16] "scl017161.17_109-S"  "scl55032.7_30-S"     "scl018293.8_37-S"   
[19] "scl28971.3_6-S"      "scl31346.12.1_18-S"  "scl0002319.1_93-S"  
[22] "scl42057.12_19-S"    "scl33796.16.1_75-S"  "scl056720.1_140-S"  
[25] "scl17254.11_24-S"    "scl19475.14.1_7-S"   "scl0070560.2_290-S" 
[28] "scl070560.6_1-S"     "scl20979.15_678-S"   "scl0001350.1_72-S"  
[31] "scl0001351.1_1-S"    "scl0001460.1_23-S"   "scl0001552.1_33-S"  
[34] "scl0001564.1_6-S"    "scl071562.11_5-S"    "scl25468.2_282-S"   
[37] "scl48651.6_179-S"    "scl30075.6.1_112-S"  "scl30519.4.1_41-S"  
[40] "scl26754.19_121-S"   "scl098256.13_10-S"   "scl17183.1.57_1-S"  
[43] "scl25034.6_52-S"     "scl0001706.1_11-S"   "scl0001737.1_18-S"  
[46] "scl49555.11.1_9-S"   "scl0002878.1_54-S"   "scl54377.16.1_8-S"  
[49] "scl35850.12_191-S"   "scl0110460.1_24-S"   "scl51398.20_59-S"   
[52] "scl0209176.1_37-S"   "scl37491.11.1_193-S" "scl0002087.1_19-S"  
[55] "scl0229905.15_25-S"  "GI_38075901-S"       "scl17534.5.1_27-S"  
[58] "scl000730.1_110-S"   "scl34554.11.1_42-S" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>