An annotation data object that maps Entrez Gene identifiers to Reactome pathway identifiers

Description

reactomeEXTID2PATHID maps Entrez Gene identifiers to Reactome pathway identifiers.

Details

This is an R object containing key and value pairs. Keys are Entrez Gene identifiers and values are the corresponding Reactome 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 Reactome pathway identifiers.

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

Mappings between Reactome pathway identifiers and pathway names can be obtained through another annotation data object named reactomePATHID2NAME.

Mappings were based on data provided by: Reactome http://www.reactome.org/download/current/sql.gz & http://www.reactome.org/download/current/sql_dn.gz With a date stamp from the source of: 2010-Dec-21

References

http://www.reactome.org/

Examples

	xx <- as.list(reactomeEXTID2PATHID)
	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.
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(reactome.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/reactome.db/reactomeEXTID2PATHID.Rd_%03d_medium.png", width=480, height=480)
> ### Name: reactomeEXTID2PATHID
> ### Title: An annotation data object that maps Entrez Gene identifiers to
> ###   Reactome pathway identifiers
> ### Aliases: reactomeEXTID2PATHID
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 	xx <- as.list(reactomeEXTID2PATHID)
> 	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]
+ 		}
+ 	}
$`10898`
 [1] "168276"  "1643685" "168253"  "5663205" "168254"  "168315"  "168276" 
 [8] "1643685" "168253"  "5663205" "168254"  "168315" 

$`8106`
 [1] "168276"  "109688"  "1643685" "74160"   "168253"  "5663205" "168254" 
 [8] "168315"  "72187"   "72172"   "72163"   "112296"  "112297"  "76044"  
[15] "72203"   "75067"   "77595"   "73857"   "73856"   "74159"   "168276" 
[22] "109688"  "1643685" "74160"   "168253"  "5663205" "168254"  "168315" 
[29] "72187"   "72172"   "72163"   "112296"  "112297"  "76044"   "72203"  
[36] "75067"   "77595"   "73857"   "73856"   "74159"  

$`5610`
 [1] "168276"  "1643685" "168253"  "5663205" "168254"  "169131"  "168276" 
 [8] "1643685" "168253"  "5663205" "168254"  "169131" 

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