Files in netDx

Network-based patient classifier

README.md tests/testthat.R tests/testthat/test_buildpredictor.R tests/testthat/test_suite.R R/sparsify2.R R/getEmapInput_many.R R/makeQueries.R R/getPatientRankings.R R/Nets_writeSIF.R R/perfCalc.R R/makePSN_NamedMatrix.R R/enrichLabelNets.R R/buildPredictor_sparseGenetic.R R/writeQueryBatchFile.R R/getPatientPredictions.R R/predictPatientLabels.R R/plotIntegratedPatientNetwork.R R/getRegionOL.R R/similarities.R R/utils.R R/sparsify3.R R/updateNets.R R/createPSN_MultiData.R R/writeWeightedNets.R R/runQuery.R R/pruneNets.R R/writeQueryFile.R R/makeSymmetric.R R/getCorrType.R R/buildPredictor.R R/fileCache.R R/countPatientsInNet.R R/RR_featureTally.R R/getEmapInput.R R/dataList2list.R R/callFeatSel.R R/mapNamedRangesToSets.R R/runProfileToNetworks.R R/compareShortestPath.R R/runFeatureSelection.R R/matrix_getIJ.R R/cleanPathwayName.R R/plotPerf_multi.R R/getSimilarity.R R/moveInteractionNets.R R/pruneNetByStrongest.R R/pruneNet_pctX.R R/makePSN_RangeSets.R R/compileFeatureScores.R R/setupFeatureDB.R R/compileFeatures.R R/getFeatureScores.R R/plot_tSNE.R R/splitTestTrain_partition.R R/randAlphaNum.R R/globals.R R/splitTestTrain_resampling.R R/plotEmap.R R/smooMutationPropagation.R R/readPathways.R R/getNetConsensus.R R/sparsenet_enrichment_functions.R R/plotPerf.R R/simpleCap.R man/thresholdSmoothedMutations.Rd man/getPatientRankings.Rd man/writeNetsSIF.Rd man/makePSN_RangeSets.Rd man/compareShortestPath.Rd man/makeQueries.Rd man/fetchPathwayDefinitions.Rd man/plot_tSNE.Rd man/getFeatureScores.Rd man/setupFeatureDB.Rd man/cnv_netScores.Rd man/mapNamedRangesToSets.Rd man/dot-get_cache.Rd man/getEMapInput.Rd man/predictPatientLabels.Rd man/pheno_full.Rd man/countPatientsInNet.Rd man/getEMapInput_many.Rd man/sim.pearscale.Rd man/pruneNets.Rd man/convertProfileToNetworks.Rd man/plotPerf.Rd man/sim.eucscale.Rd man/cleanPathwayName.Rd man/npheno.Rd man/buildPredictor_sparseGenetic.Rd man/getRegionOL.Rd man/getNetConsensus.Rd man/sparsify3.Rd man/genes.Rd man/plotIntegratedPatientNetwork.Rd man/writeQueryBatchFile.Rd man/pheno.Rd man/MB.pheno.Rd man/countIntType.Rd man/runFeatureSelection.Rd man/getPatientPredictions.Rd man/callFeatSel.Rd man/runQuery.Rd man/featScores.Rd man/getOR.Rd man/splitTestTrain.Rd man/pruneNet_pctX.Rd man/compileFeatureScores.Rd man/perfCalc.Rd man/matrix_getIJ.Rd man/simpleCap.Rd man/cnv_TTstatus.Rd man/predRes.Rd man/smoothMutations_LabelProp.Rd man/enrichLabelNets.Rd man/getEnr.Rd man/sparsify2.Rd man/pathwayList.Rd man/buildPredictor.Rd man/makePSN_NamedMatrix.Rd man/getFileSep.Rd man/normDiff.Rd man/silh.Rd man/randAlphanumString.Rd man/cnv_netPass.Rd man/getSimilarity.Rd man/RR_featureTally.Rd man/plotPerf_multi.Rd man/moveInteractionNets.Rd man/cnv_pheno.Rd man/plotEmap.Rd man/cnv_GR.Rd man/pathway_GR.Rd man/dataList2List.Rd man/confmat.Rd man/xpr.Rd man/makeSymmetric.Rd man/compileFeatures.Rd man/avgNormDiff.Rd man/updateNets.Rd man/pruneNet.Rd man/getCorrType.Rd man/countIntType_batch.Rd man/cnv_patientNetCount.Rd man/readPathways.Rd man/splitTestTrain_resampling.Rd man/writeQueryFile.Rd man/getGMjar_path.Rd man/writeWeightedNets.Rd man/createPSN_MultiData.Rd inst/doc/ThreeWayClassifier.Rmd inst/doc/BuildPredictor.Rmd inst/doc/BuildPredictor.R inst/doc/ThreeWayClassifier.R inst/doc/Predict_CaseControl_from_CNV.R inst/doc/Predict_CaseControl_from_CNV.Rmd vignettes/ThreeWayClassifier.Rmd vignettes/RaggedExperiment_example.R vignettes/BuildPredictor.Rmd vignettes/Predict_CaseControl_from_CNV.Rmd