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Last data update: 2014.03.03

R: Convert KEGG identifiers to/from outside identifiers

keggConv

R Documentation

Convert KEGG identifiers to/from outside identifiers

Description

Convert KEGG identifiers to/from outside identifiers.

Usage

keggConv(target, source)

Arguments

`target`	A KEGG organism code (), T number, or one of the external databases `ncbi-gi`, `ncbi-geneid`, `ncbi-proteinid`, `uniprot`, or (for chemical substance identifiers) `drug`, `compound`, or `glycan`, `pubchem`, or `chebi`.
`source`	Same as `target`, but may also be a list of KEGG identifers representing internal or external names.

Value

A named character vector.

Author(s)

Dan Tenenbaum

References

http://www.kegg.jp/kegg/docs/keggapi.html

Examples

head(keggConv("eco", "ncbi-geneid")) ## conversion from NCBI GeneID to 
                               ## KEGG ID for E. coli genes
head(keggConv("ncbi-geneid", "eco")) ## opposite direction
head(keggConv("ncbi-proteinid", c("hsa:10458", "ece:Z5100"))) ## conversion from KEGG ID
                                                 ## to NCBI GI
## conversion from NCBI GI to KEGG ID when the organism code is not known:
head(keggConv("genes", "ncbi-geneid:3113320"))

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(KEGGREST)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGREST/keggConv.Rd_%03d_medium.png", width=480, height=480)
> ### Name: keggConv
> ### Title: Convert KEGG identifiers to/from outside identifiers
> ### Aliases: keggConv conv bconv
> ### Keywords: conv
> 
> ### ** Examples
> 
> head(keggConv("eco", "ncbi-geneid")) ## conversion from NCBI GeneID to 
ncbi-geneid:944742 ncbi-geneid:945803 ncbi-geneid:947498 ncbi-geneid:945198 
       "eco:b0001"        "eco:b0002"        "eco:b0003"        "eco:b0004" 
ncbi-geneid:944747 ncbi-geneid:944749 
       "eco:b0005"        "eco:b0006" 
>                                ## KEGG ID for E. coli genes
> head(keggConv("ncbi-geneid", "eco")) ## opposite direction
           eco:b0001            eco:b0002            eco:b0003 
"ncbi-geneid:944742" "ncbi-geneid:945803" "ncbi-geneid:947498" 
           eco:b0004            eco:b0005            eco:b0006 
"ncbi-geneid:945198" "ncbi-geneid:944747" "ncbi-geneid:944749" 
> head(keggConv("ncbi-proteinid", c("hsa:10458", "ece:Z5100"))) ## conversion from KEGG ID
                 hsa:10458                  ece:Z5100 
"ncbi-proteinid:NP_059345"  "ncbi-proteinid:AAG58814" 
>                                                  ## to NCBI GI
> ## conversion from NCBI GI to KEGG ID when the organism code is not known:
> head(keggConv("genes", "ncbi-geneid:3113320"))
character(0)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>