cMAPCARTAINTERACTION {cMAP} | R Documentation |
cMAPCARTAINTERACTION maps cMAP (NCICB Pathway Interaction Database) molecule ids to data about the interactions of the molecule represented by the ids and other 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 source, process, reversible, condition, and component element.
The source element is a character string indicating whether the interactions between molecules are from a BioCarta or KEGG pathway.
The process is a character string describing the process the key molecule is involved. Potential values include "reaction", "modification", "transcription", "translocation", "macroprocess" or a more specific subtype of macroprocess including any term from the GO Biological Process vocabulary.
The reversible element is a boolean indicating whether the interaction is reversible.
The condition element is a character string indicating the biological process the interactions take place. Potential values include any term from the GO Biological Process vocabulary.
The component element contains sublists of vectors. Each key molecule id has a sequence of component represented by elements of the sublist. Each sublist has an id (molecule id of the interacting molecule), edge (indicating the way two molecule interact. Potential values include "input", "agent", "inhibitor", and "output"), role (the function of the key molecule. Potential values include any term from the GO Molecular Function vocabulary), location (a GO Cellular Component vocabulary indicating the location of the interaction), and activity (an abstract term that can be "inactive", "active", "active1", "active2") elements.
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(cMAPCARTAINTERACTION) 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] } }