AddLogicGates           extend model with node representing logic gate
CreateExtendedAdjacency
                        Create an extended adjacency matrix
CreateRandomGraph       Create a random graph
CreateTopology          create topology for a randomly generated
                        pathway topology
ExtendTopology          Extending topology of normal "nem"
GenerateData            Generate data from extended model. Given a
                        model created from CreateTopology and
                        ExtendTopology, this function creeates
                        acorresponding artificial data matrix, which is
                        used as a ground truth for simulation studies.
HeatmapOP               heatmap function based on the lattice package
                        more information: ?xyplot
Mll                     Evaluation of graphs
SimEpiNEM               Compares different network reconstruction
                        algorithm on simulated data.
epiAnno                 Plots logical gate data annotation. The 8
                        heatmaps visualize what perfect data would look
                        like in respective to each logical gate.
                        Perfect data is equivalent to Boolean truth
                        tables.
epiNEM                  Epistatic NEMs - main function. This function
                        contains the inference algorithm to learn
                        logical networks from knock-down data including
                        double knock-downs.
epiScreen               This function is used to analyse knock-out
                        screens with multiple double and single
                        knock-outs combined in one data set.
plot.epiNEM             Plots the winning pathway structure
plot.epiScreen          Plots the sresults of a systematic knock-out
                        screen
plot.epiSim             Plots the simulation results
sameith_GO              graph-based GO similarity scores, string GO
                        annotations for Sameith et al., 2015 data The
                        data consists of lists including epiNEM
                        identified and general similarity scores and GO
                        annotations for each triple. For details see
                        the vignette.
sameith_string          sig. of string interaction scores for Sameith
                        et al., 2015 data The data consists of a list
                        including a vectors of pairs (for interactions)
                        and a corresponding list of interaction scores
                        derived form the string database. For details
                        see the vignette.
samscreen               Example data: epiNEM results for the Sameith et
                        al., 2015 knock-out screen The result of the
                        epiNEM analysis of the data from
                        "http://www.holstegelab.nl/publications/
                        sv/signaling_redundancy/downloads/DataS1.txt".
                        The data consists of a list of matrices with
                        the likelihoods (ll) for each analysed triple
                        of signalling genes and the inferred logic
                        (logic) for each triple. The signalling genes
                        or modulators C are the rows and the signalling
                        genes from the double knock-downs are in the
                        columns. For details see the vignette.
sim                     Example data: simulation results Contains
                        simulation results. How they were aquired is
                        explained in the vignette. The data conists of
                        a list of data matrices holding sensitivity and
                        specificity (spec, sens) of network edges for
                        the variious methods compared to the ground
                        truth, sensitivity and specificity (sens2,
                        spec2) of the expected data for epiNEM and
                        Boolean NEMs and accuracy of the inferred
                        logics for both. The different methods are in
                        the rows and the columns denote the different
                        independent simulation runs.
wageningen_GO           graph-based GO similarity scores, string GO
                        annotations for van Wageningen et al., 2015
                        data The data consists of lists including
                        epiNEM identified and general similarity scores
                        and GO annotations for each triple. For details
                        see the vignette.
wageningen_string       sig. of string interaction scores for van
                        Wageningen et al., 2010 data The data consists
                        of a list including a vectors of pairs (for
                        interactions) and a corresponding list of
                        interaction scores derived form the string
                        database. For details see the vignette.
wagscreen               Example data: epiNEM results for the Wageningen
                        et al., 2010 knock-out screen
                        "http://www.holstegelab.nl/publications/GSTF_geneticinteractions/
                        downloads/del_mutants_limma.txt" The data
                        consists of a list of matrices with the
                        likelihoods (ll) for each analysed triple of
                        signalling genes and the inferred logic (logic)
                        for each triple. The signalling genes or
                        modulators C are the rows and the signalling
                        genes from the double knock-downs are in the
                        columns. For details see the vignette.
