get.similarity.between.genes {KEGGSOAP}R Documentation

Client-side interface to obtain the similarity value between two genes

Description

Given two KEGG ids for genes, the function searches the KEGG GENES database to obtain a measure of the similarity between the two genes. The similarity between genes is determined by alignment of matching bases.

Usage

get.similarity.between.genes(genes.id1, genes.id2)

Arguments

genes.id1 genes.id1 a character string for the id used by KEGG to represent the gene of interest. The id normally consists of three letters followed by a colon and then several 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)
genes.id2 genes.id2 same as genes.id1 but for another gene

Details

The corresponding KEGG SOAP method returns a list of data as described in the return list of get.best.neighbors.by.gene. get.similarity.between.genes extracts and returns the value for identity from the list.

Value

This function returns a value between 0 and 1 for the protortion of matching bases between the two genes

Author(s)

Jianhua Zhang

References

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

See Also

get.neighbors.by.gene

Examples

    if(require("SSOAP") && require("XML")){
        get.similarity.between.genes("eco:b0002", "eco:b3940")
    }

[Package KEGGSOAP version 0.6.5 Index]