updateOrgEnvir: Update the organism-specific environment variables

In SubpathwayGMir: Identify Metabolic Subpathways Mediated by MicroRNAs

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).

Author(s)

Li Feng, Chunquan Li and Xia Li

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)

SubpathwayGMir documentation built on May 2, 2019, 2:39 a.m.