PKNlist-class: K/P-S network

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

K/P-S network

Description

This class contains the background of K/P-S interactions networks

Objects from the Class

Objects of class PKNlist can be created from new("KPSbg", interactions=allD, species=unique(c(allD$K.ID, allD$S.cc)))

Slots

interactions:

an interactions data frame

interactionsD:

a subset of interactions that only contains experimentally supported direct interactions between drug targets and data points

species:

a character vector of nodes

sinks:

a character vector of sink nodes

integrators:

a character vector of integrator nodes

intermediates:

a character vector of intermediate nodes

Methods

An overview of methods with class-specific functionality: More detailed introduction can be found in help for each specific function.

buildPKN

build a PKN for a specific data set, from a full background network

PKNlist

create the PKNlist from a PKN created by buildPKN

Author(s)

C. Terfve [e-mail]

See Also

buildPKN PKNlist

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