| create.pathway.node.attributes | R Documentation |
This function writes a standard Cytoscape node attribute list (http://www.cytoscape.org/) file. It takes the compound codes and retrieve all the known pathways, where the compound is known to be present. It only works for KEGG, but, a specification of database will be available soon.
create.pathway.node.attributes(classTable, graph, DB,
filename1, filename2 = NULL, organismId = NULL)
classTable |
classification table created by export.class.table function. |
graph |
graphNEL object, with node indexes corresponding to mass indexes in classTable. |
DB |
database with compound names associated to unique ids, used by export.class.table function. |
filename1 |
filename to attribute pathway list file. |
filename2 |
optional filename to attribute pathway list discriminating compound/pathway associations. |
organismId |
KEGG organism id (http://www.kegg.jp/kegg/catalog/org_list.html) to filter possibibly pathwyas for known pathways for that organism. |
writes a standard Cytoscape attribute list to current working directory. Also creates a matrix containing putative compound counting to each pathway.