NAMESPACE

# Generated by roxygen2: do not edit by hand

export(RR_featureTally)
export(avgNormDiff)
export(buildPredictor)
export(buildPredictor_sparseGenetic)
export(callFeatSel)
export(callOverallSelectedFeatures)
export(cleanPathwayName)
export(compareShortestPath)
export(compileFeatureScores)
export(compileFeatures)
export(confusionMatrix)
export(convertProfileToNetworks)
export(convertToMAE)
export(countIntType)
export(countIntType_batch)
export(countPatientsInNet)
export(createNetFuncFromSimList)
export(createPSN_MultiData)
export(dataList2List)
export(enrichLabelNets)
export(fetchPathwayDefinitions)
export(getEMapInput)
export(getEMapInput_many)
export(getEnr)
export(getFeatureScores)
export(getFileSep)
export(getGMjar_path)
export(getNetConsensus)
export(getOR)
export(getPSN)
export(getPatientPredictions)
export(getPatientRankings)
export(getPerformance)
export(getRegionOL)
export(getResults)
export(getSimilarity)
export(makeInputForEnrichmentMap)
export(makePSN_NamedMatrix)
export(makePSN_RangeSets)
export(makeQueries)
export(makeSymmetric)
export(mapNamedRangesToSets)
export(normDiff)
export(perfCalc)
export(plotEmap)
export(plotIntegratedPatientNetwork)
export(plotPerf)
export(plotPerf_multi)
export(predict)
export(predictPatientLabels)
export(pruneNet)
export(pruneNet_pctX)
export(pruneNets)
export(randAlphanumString)
export(readPathways)
export(runFeatureSelection)
export(runQuery)
export(setupFeatureDB)
export(sim.eucscale)
export(sim.pearscale)
export(simpleCap)
export(smoothMutations_LabelProp)
export(sparsify2)
export(sparsify3)
export(splitTestTrain)
export(splitTestTrain_resampling)
export(subsampleValidationData)
export(tSNEPlotter)
export(thresholdSmoothedMutations)
export(updateNets)
export(writeNetsSIF)
export(writeQueryBatchFile)
export(writeQueryFile)
export(writeWeightedNets)
import(BiocFileCache)
import(GenomicRanges)
import(MultiAssayExperiment)
import(ROCR)
import(Rtsne)
import(bigmemory)
import(doParallel)
import(foreach)
import(ggplot2)
import(glmnet)
import(parallel)
import(pracma)
import(reshape2)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,seqlevels)
importFrom(GenomicRanges,GRanges)
importFrom(IRanges,IRanges)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(combinat,combn)
importFrom(ggplot2,ggplot)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,hist)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,segments)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(httr,HEAD)
importFrom(igraph,E)
importFrom(igraph,delete.edges)
importFrom(igraph,edge_attr)
importFrom(igraph,get.edgelist)
importFrom(igraph,graph_from_data_frame)
importFrom(methods,is)
importFrom(methods,slotNames)
importFrom(plotrix,color2D.matplot)
importFrom(pracma,trapz)
importFrom(rappdirs,user_cache_dir)
importFrom(reshape2,melt)
importFrom(stats,aggregate)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,density)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,qexp)
importFrom(stats,sd)
importFrom(stats,wilcox.test)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,write.table)