SubpathwayGMir (version 1.0)

updateOrgEnvir: Update the organism-specific environment variables

Description

Update the organism-specific environment variables that user interested.

Usage

updateOrgEnvir(org = "hsa", path = "http://rest.kegg.jp", verbose = TRUE)

Arguments

org

A character string. It supports six species and must be the abbreviation of a genome name, such as cel(caenorhabditis elegans), dme(drosophila melanogaster), dre(danio rerio), hsa(homo sapiens), mmu(mus musculus) and rno(rattus norvegicus).

path

A character string. The reference path for downloading organism-specific data.

verbose

A logical. If TRUE, the additional diagnostics are printed.

Details

This package supports to identify metabolic subpathways among six organisms. We only need to update the organism-specific environment variables before subpathway identification. The six organisms contain cel(caenorhabditis elegans), dme(drosophila melanogaster), dre(danio rerio), hsa(homo sapiens), mmu(mus musculus) and rno(rattus norvegicus). The defalut value of the argument org is "hsa" (human).

Examples

## Not run: 
# 
# ## update organism and the type of gene identifiers ##
#  
#  updateOrgEnvir("mmu")
#  
# # show the current environment variables
#  ls(k2ri)
# 
# # show the background of miRNAs
#  k2ri$BGMiRNA[1:3]
# ## End(Not run)