buildPKN: Make a starting network

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

Make a starting network

Description

This function makes a starting network based on data, a kinase substrate interaction data frame and a list of drug targets

Usage

buildPKN(data.On,targets.On, bg,nK=c("all","no", "drugs2data", "data"))

Arguments

data.On	a GMMbyCond object as created by dataBycond
targets.On	a list of drug targets (Uniprot identifiers matching to the "K.ID" column in the background network data frame)
bg	a KPSbg object that contains all interactions that can be considered to make a background network, e.g. made from the allD data frame resulting from the database combination process. The original interactions data frame must have at least the following columns: the "K.ID" column (kinase Uniprot ID) and the "S.ID" column (substrate Uniprot ID), the "SID" column (unique character string identifiers for interactions), the "S.cc" column (substrateUPID.res.pos)
nK	a single string ("all","no", "drugs2data", "data") specifying whether the predicted edges should be included at all levels, none, only in the network that connects drug targets to data kinases or only between data sites and their kinases

Details

If you add data to our network beyond the automatically provided one, the column "SID" needs to be filled, as any row with NA in that column will be removed (the weight correction depends on unique identifiers in that column).

Value

This function returns a new KPSbg object that contains all interactions linking drug targets and drug targets to perturbed sites, and additional edges for integrator nodes (with SID="i…")

Author(s)

C. Terfve

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