KEGGPkgbuilder {AnnBuilder}R Documentation

A function to make the data package for KEGG

Description

This function generates a data package with rda files mapping KEGG pathway or enzyme names to ids and vice versa. The source files for making the mapping are from the Internet.

Usage

KEGGPkgBuilder(pkgPath, pkgName = "KEGG", version = "1.0.1", pathwayURL
= getKEGGFile("path"), enzymeURL = getKEGGFile("enzyme"), geneMapURL =
getKEGGFile("geneMap"), force = TRUE, author = list(author = "who",
maintainer = "who@email.com"))  
getEIdNName(enzymeURL)
getKEGGFile(whichOne, organism = "hsa")
getKEGGGeneMap(organism = "Homo sapiens"))

Arguments

pkgPath A character string for the name of path to which the data package will be stored.
pkgName A character string for the name of the data package.
version A character string for the version number of the system by which the data package is generated.
pathwayURL A character string for the URL where the source file for pathway data will be downloaded.
enzymeURL A character string for the URL from which the source file for enzyme data will be downloaded.
geneMapURL A character string for the URL from which the source file for the_gene_map.tab data file that will be used to build the mappings between external gene ids (LocusLink or ORF) to pathway ids.
force A boolean to indicate whether the existing data package will be over written.
whichOne A charcter string for the name of file type. Valid values include "path" or "enzyme"
author A list of character strings with one element being name for the name of the author and another being address being the email address of the author
organism organism a character string for the name of the organism of interest

Details

The data package produced will have the normal structure of an R package (i. g. with R, man, data, and src directories) under a directory defined by pkgName under pkgPath.

Value

This function does not return any value.

Note

This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R.

Author(s)

Jianhua Zhang

References

An Introduction to R - Writting R Extensions.

See Also

package.skeleton

Examples

# To be added

[Package AnnBuilder version 1.4.21 Index]