pathsD: Max scoring path

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

Max scoring path

Description

Extracts, from a background network with optimised weights, the maximum scoring paths from a kinase to a set of data nodes

Usage

pathsD(nwTable, nM,nodes2link,drug)

Arguments

nwTable	a background network data frame (from interactions(pknList)), with appropriate optimised weights in the ntag column (this is what is used to decide on the max input)
nM	the number of models on which the frequency is based
nodes2link	a character vector of data nodes that we want to connect
drug	a single character string, containing the name of the K/P that we want to connect (a single UPID)

Details

The maximum input edge is picked based on the "ntag" column of the nwTable data frame, so it should contain opres$FE[match(nwTable$SID, rownames(opres$FE)),dim(opres$FE)[2]] where opres is the list resulting from the oRes function. If we are working with combined optimisations, then the ntag column should contained the averaged equivalents of the vector just mentioned.

Value

a data frame of interactions that is a subset of the starting one

Author(s)

C. Terfve

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