cMapPathBuilder {AnnBuilder}R Documentation

Functions that build a data pacakge using data provided by cMAP

Description

NCICB Pathway Interaction Database provides two data files molecule interaction data for BioCarta and KEGG pathways. The functions described here use the two files and build a data package containing the data

Usage

cMapPathBuilder(cartaName, keggName, pkgName = "cMAP", pkgPath, version
= "1.1.0", author = list(author = "anonymous", maintainer =
"anonymous@email.com"))
cMAPParser(sourceFile)  

Arguments

cartaName cartaName a character string for the name of the XML file containing data for BioCarta pathways
keggName keggName a character string for the name of the XML file containing data for BioCarta pathways
pkgName pkgName a character string for the name of the package to be built
pkgPath pkgPath a character string for the path to the directory where the new package to built will reside
version version a character string for the version number of package to be built
author author a list with an author and maintainer element for the name and email address of the author of the pacakge
sourceFile sourceFile a character string for the name of the source data for BioCarta or KEGG

Details

cMAP currently does not support ftp downloading of the source data file. The files to be used have to be downloaded through a web browser and the name (with full path) of the downloaded file will be used.

Value

cMapPathBuilder returns a list with three elements:

molecule a list of vectors/lists containing molecule data
interaction a list of vectors/lists containing molecule interaction data
pathway a list of vectors containing pathway component data

Note

Author(s)

Jianhua Zhang

References

http://cmap.nci.nih.gov/PW/

Examples

## No example is provided

[Package AnnBuilder version 1.4.21 Index]