Files in netDx
Network-based patient classifier

LICENSE
.BBSoptions
NEWS
NAMESPACE
DESCRIPTION
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/extdata/TGCT_mutSmooth_pheno.txt
inst/extdata/pathways.gmt
inst/extdata/genemania.xml
inst/extdata/TGCT_mutSmooth_geno.txt
inst/extdata/GM_query.txt
inst/extdata/AGP1_CNV.txt
inst/extdata/example_output/inputNets.txt
inst/extdata/example_output/rng3/predictionResults.txt
inst/extdata/example_output/rng3/notLumA/GM_results/notLumA_pathway_CV_score.txt
inst/extdata/example_output/rng3/LumA/GM_results/LumA_pathway_CV_score.txt
inst/extdata/example_output/rng1/predictionResults.txt
inst/extdata/example_output/rng1/notLumA/GM_results/notLumA_pathway_CV_score.txt
inst/extdata/example_output/rng1/LumA/GM_results/LumA_pathway_CV_score.txt
inst/extdata/example_output/rng2/predictionResults.txt
inst/extdata/example_output/rng2/notLumA/GM_results/notLumA_pathway_CV_score.txt
inst/extdata/example_output/rng2/LumA/GM_results/LumA_pathway_CV_score.txt
inst/extdata/GM_NRANK/CV_2.query-results.report.txt.NRANK
inst/extdata/GM_NRANK/CV_1.query-results.report.txt.NRANK
inst/extdata/example_nets/SMALL_CONTROL.txt
inst/extdata/example_nets/SMALL_CASE.txt
inst/extdata/example_nets/BOTH_EQUAL.txt
inst/extdata/example_nets/BIG_CONTROL.txt
inst/extdata/example_nets/MOSTLY_CASE.txt
inst/extdata/example_nets/BIG_CASE.txt
inst/extdata/INSTALL/Dockerfile
inst/extdata/INSTALL/INSTALL_OSX.sh
inst/extdata/INSTALL/INSTALL_Unix.sh
inst/extdata/dbPath/genemania.xml
inst/extdata/dbPath/user/segments.gen
inst/extdata/dbPath/user/segments_1
inst/extdata/dbPath/base/_0.cfs
inst/extdata/dbPath/base/segments_2
inst/extdata/dbPath/base/segments.gen
inst/extdata/dbPath/1/_0.cfs
inst/extdata/dbPath/1/segments_2
inst/extdata/dbPath/1/metadata.xml
inst/extdata/dbPath/1/segments.gen
inst/extdata/dbPath/cache/CORE/1/attributeGroups.ser
inst/extdata/dbPath/cache/CORE/1/1.ser
inst/extdata/dbPath/cache/CORE/1/networkIds.ser
inst/extdata/dbPath/cache/CORE/1/4.ser
inst/extdata/dbPath/cache/CORE/1/3.ser
inst/extdata/dbPath/cache/CORE/1/DatasetInfo.ser
inst/extdata/dbPath/cache/CORE/1/nodeIds.ser
inst/extdata/dbPath/cache/CORE/1/2.ser
inst/extdata/GM_PRANK/CV_2.query-results.report.txt.PRANK
inst/extdata/GM_PRANK/CV_1.query-results.report.txt.PRANK
inst/extdata/plots/SURVIVEYES.gmt
inst/extdata/plots/SURVIVEYES_nodeAttrs.txt
inst/extdata/plots/SURVIVENO.gmt
inst/extdata/plots/SURVIVENO_nodeAttrs.txt
inst/doc/ThreeWayClassifier.Rmd inst/doc/BuildPredictor.Rmd
inst/doc/Predict_CaseControl_from_CNV.html
inst/doc/BuildPredictor.R inst/doc/ThreeWayClassifier.R inst/doc/Predict_CaseControl_from_CNV.R
inst/doc/ThreeWayClassifier.html
inst/doc/BuildPredictor.html
inst/doc/Predict_CaseControl_from_CNV.Rmd
data/xpr.rda
data/predRes.rda
data/cnv_pheno.rda
data/confmat.rda
data/silh.rda
data/cnv_netScores.rda
data/cnv_netPass.rda
data/genes.rda
data/cnv_TTstatus.rda
data/cnv_patientNetCount.rda
data/npheno.rda
data/cnv_GR.rda
data/pathway_GR.rda
data/pheno.rda
data/MB.pheno.rda
data/pheno_full.rda
data/pathwayList.rda
data/featScores.rda
build/vignette.rds
vignettes/ThreeWayClassifier.Rmd vignettes/RaggedExperiment_example.R vignettes/BuildPredictor.Rmd
vignettes/integratedPSN_MEAN_top0.10.png
vignettes/Emap_example_screenshot.png
vignettes/EMap_realworld.png
vignettes/Predict_CaseControl_from_CNV.Rmd
netDx documentation built on Dec. 11, 2020, 2:01 a.m.