get.genes.by.organism {KEGGSOAP}R Documentation

Client-side interface to obtain the KEGG ids for all the genes of a given organism

Description

Given a KEGG organism id, the function searches the KEGG GENES database for all the genes of the organism

Usage

get.genes.by.organism(org, start, max.results)

Arguments

org org a character string for the id used by KEGG for organisms. The organism ids are normally three-letter codes with the first letter being the first letter of the genus name and the rest being the first two letters of the species name of the scientic name of the organism of concern
start start an integer to indicate the location of the entry in the query results from which the results will be extracted and returned
max.results max.results an integer to indicate the maximum number of entries that will be extracted from the query results and returned

Details

The gene ids returned by the query normally consist of three letters followed by a colon and then numbers or a combination of letters and numbers. The three letters are from the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern (e. g. hsa:111 for Homo Sapiens)

Value

The function returns a vector of character strings of ids used by KEGG to represent genes

Author(s)

Jianhua Zhang

References

http://www.genome.jp/kegg/soap/doc/keggapi_manual.html

Examples

   if(require("SSOAP") && require("XML")){
        genes <- get.genes.by.organism("hsa", 1, 10)
    }

[Package KEGGSOAP version 1.4.0 Index]