assignAttributes: Assigning node attributes

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

Assigning node attributes

Description

This function assigns attributes to each node in the PHONEMeS solution (D - whether a node is a drug target; P - whther a node is a measured site; while the other nodes which have no attribute assigned are the ones that are inferred by PHONEMeS). This function is used anly to assist the visualization of the PHONEMeS solutions in CytoScape.

Arguments

sif	the PHONEMeS solution as a matrix of interactions with three columns (Target, Source and Weight)
inputObj	the PHONEMeS data inputs that were used for the analysis
targets	the list of drug perturbation targets
writeAttr	a verbose (TRUE/FALSE) indicating whether to write the attributes as a txt file
fileName	the name of the file and the path where to save the txt files of the attributes

Value

This function returns a matrix with two columns where in the first column we have the node ID's and on the second column we have the attributes assigned (D, P or none)

Author(s)

E. Gjerga

saezlab/PHONEMeS-ILP documentation built on June 21, 2022, 5:36 p.m.