create.reaction.edge.attributes: create.reaction.edge.attributes

In rsilvabioinfo/ProbMetab: Probabilistic annotation of LC-MS based metabolomics

Description

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.

Usage

  create.reaction.edge.attributes(classTable, graph, w,
    reactionM, DB, filename)

Arguments

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.

Value

Writes a standard Cytoscape attribute list to the current working directory.

rsilvabioinfo/ProbMetab documentation built on May 28, 2019, 3:32 a.m.