| create.reaction.edge.attributes | R Documentation |
This function writes a standard Cytoscape edge attribute list (http://www.cytoscape.org/) file. It takes the the possible mass connections, codified w matrix, retrieve the reactions where the compound is known to be present and associate then to a mass edge. It only works for KEGG, but, a specification of database will be available soon.
create.reaction.edge.attributes(classTable, graph, w,
reactionM, DB, filename)
classTable |
classification table created by export.class.table function. |
graph |
graphNEL object, with node indexes corresponding to mass indexes in classTable. |
w |
matrix of compound connections. |
reactionM |
data.frame with compound annotation information. |
DB |
database with compound names associated to unique ids, used by export.class.table function. |
filename |
reaction attribute list file. |
Writes a standard Cytoscape attribute list to the current working directory.