cMAPKEGGPATHWAY {cMAP}R Documentation

An annotation data file that maps cMAP short pathway names to descriptive data about the pathway

Description

cMAPKEGGPATHWAY maps cMAP (NCICB Pathway Interaction Database) abbreviated pathway names to descriptive data about the pathway

Details

This is an environment object containing key and value pairs. Keys are short pathway names and values are lists of vectors. Each pathway name is mapped to a list that has an identifier. name, organism, source, and component element.

The identifier element is an integer for NCICB Pathway Interaction Database identifier.

The name element is the full length of textual descriptive name for the pathway.

The organism is a character string for an abbreviation of organism name (e. g. Hs = human)

The source element is a character string indicating whether the interaction is a BioCarta or KEGG pathway.

The type element is a character string describing what type of molecule the key molecule identifier corresponds to. Potential values for type include "protein", "complex", "compound", and "rna".

The component element is a vector of integers for the identifiers of molecules that are involved in the pathway.

Mappings were based on data provided by:

cMAP: http://cmap.nci.nih.gov/PW/Download. Build: Unavailable. Downloaded:Tue Sep 12 16:52:56 2006

Package built: Tue Sep 12 16:52:56 2006

References

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

Examples

    require(cMAP) || stop(paste(cMAP, "unavailable"))
    xx <- as.list(cMAPKEGGPATHWAY)
    if(length(xx) > 0){
        # Get the value of the first key
        xx[[1]]
        # Get the values for multiget for a few keys
        if(length(xx) >= 3){
            xx[1:3]
        }
    }

[Package cMAP version 1.15.1 Index]