epiNEM

Documentation for package ‘epiNEM’ version 1.12.0

AddLogicGates	Add logic.
CreateExtendedAdjacency	Create an extended adjacency matrix
CreateRandomGraph	Create a random graph
CreateTopology	Create Topology.
epiAnno	Gate visualisation.
epiNEM	Epistatic NEMs - main function.
epiScreen	Analyse large double knock-out screen.
ExtendTopology	Extending topology of normal "nem"
GenerateData	Generate data from extended model.
HeatmapOP	Heatmap.
Mll	Evaluation of graphs
plot.epiNEM	Plot pathway.
plot.epiScreen	Plot screen.
plot.epiSim	Plot simulations.
sameith_GO	graph-based GO similarity scores, string GO annotations for Sameith et al., 2015 data
sameith_string	sig. of string interaction scores for Sameith et al., 2015 data
samscreen	Example data: epiNEM results for the Sameith et al., 2015 knock-out screen
sim	Example data: simulation results
SimEpiNEM	Compare algorithms.
wageningen_GO	graph-based GO similarity scores, string GO annotations for van Wageningen et al., 2015 data
wageningen_string	sig. of string interaction scores for van Wageningen et al., 2010 data
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"