epiNEM

---

Documentation for package ‘epiNEM’ version 1.32.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
perm.rank.test	AUC permutation test
plot.epiNEM	Plot pathway.
plot.epiScreen	Plot screen.
plot.epiSim	Plot simulations.
rank.enrichment	Rank enrichment
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"