cMAPKEGGMOLECULE {cMAP} | R Documentation |
cMAPKEGGMOLECULE maps cMAP (NCICB Pathway Interaction Database) molecule ids to data about the molecules
This is an environment object containing key and value pairs. Keys are molecule ids and values are lists of vectors and sublists. Each molecule id is mapped to a list that has a type, extid, component, and member element.
The type element is a character string describing what type of molecule the key molecule id corresponds to. Potential values for type include "protein", "complex", "compound", and "rna".
The extid element is a named vector of character strings. values of the vector are external identifiers corresponding to the key molecule id. Names of the vector are abbreviations of the external public data sources from which the external ids are obtained. Potential values for vector names include "LL" (LocusLink identifier), "CA" (CAChemical Abstract number), "GO" (Gene Ontology), "KG" (KEGG), etc.
The component element is a sublist with an id (molecule id of the component molecule), location (a GO Cellular Component vocabulary indicating the location of the molecule), and activity (an abstract term that can be "inactive", "active", "active1", "active2") elements. The component element only applies to complex molecules. Each complex molecule has a sequence of component molecules represented by elements of the sublist.
The member element is a named vector of molecule ids for molecules that belong to the same protein family as the key molecule id. Names of the vector are the key molecule id.
Mappings were based on data provided by:
cMAP: http://cmap.nci.nih.gov/PW/Download. Build: Unavailable. Downloaded:Sat Mar 25 21:51:33 2006
Package built: Sat Mar 25 21:51:33 2006
cMAP http://cmap.nci.nih.gov/PW
require(cMAP) || stop(paste(cMAP, "unavailable")) xx <- as.list(cMAPKEGGMOLECULE) 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] } }