Man pages for netDx
Network-based patient classifier

avgNormDifftakes average of normdiff of each row in x
buildPredictorRun nested cross-validation on data
buildPredictor_sparseGeneticPerforms feature selection using multiple resamplings of the...
callFeatSelReturn feature selected nets based on given criteria
cleanPathwayNameClean pathway name so it can be a filename.
cnv_GRCNV locations for breast cancer (subset)
cnv_netPassList of pathway-level feature selection scores
cnv_netScoresVector of pathways that pass class enrichment
cnv_patientNetCountBinary matrix of patient occurrence in networks
cnv_phenodata.frame of patient labels and status for CNV example
cnv_TTstatuslist of train/test statuses for CNV example
compareShortestPathcompare intra-cluster shortest distance to overall shortest...
compileFeaturesCreate GeneMANIA database
compileFeatureScoresTally the score of networks through cross-validation
confmatConfusion matrix example
convertProfileToNetworksConvert profiles to interaction networks before integration
countIntTypeCounts the number of (+,+) and (+,-) interactions in a single...
countIntType_batchCounts number of (+,+) and (+,-) interactions in a set of...
countPatientsInNetCount number of patients in a network
createPSN_MultiDataWrapper to create custom input features (patient similarity...
dataList2ListConvert MultiAssayExperiment object to list and data.frame
dot-get_cachewrapper function for getting BiocFileCache associated with...
enrichLabelNetsScore networks based on their edge bias towards (+,+)...
featScoresDemo feature-level scores from running feature selection on...
fetchPathwayDefinitionsfetch pathway definitions from downloads.baderlab.org
genesTable of gene definitions (small subsample of human genes)
getCorrTypeCounts the relative correlation of (+,+) and (+,-)(-,-)...
getEMapInputwrite enrichment map for consensus nets
getEMapInput_manyWrapper to generate multiple EnrichmentMaps (perhaps one per...
getEnrGet ENR for all networks in a specified directory
getFeatureScoresCompile network scores into a matrix
getFileSepplatform-specific file separator
getGMjar_pathdownload and update GeneMANIA jar file
getNetConsensuscompile net score across a set of predictor results
getORGet relative proportion of patient classes that contribute to...
getPatientPredictionsCalculates patient-level classification accuracy across...
getPatientRankingsProcess GM PRANK files to get the ROC curve for the query
getRegionOLReturns overlapping named ranges for input ranges
getSimilarityMeasures of patient similarity
makePSN_NamedMatrixCreate patient networks from full matrix of named...
makePSN_RangeSetsCreate patient similarity interaction networks based on range...
makeQueriesRandomly select patients for queries for feature selection
makeSymmetricConvert a network in source-target-weight format to symmetric...
mapNamedRangesToSetsMap named ranges to corresponding set of named ranges
matrix_getIJConverts matrix index (1 to m*n) to row (m) and column (n)...
MB.phenoSample metadata table for medulloblastoma dataset.
moveInteractionNetsmoves interaction networks when compiling database for sparse...
normDiffSimilarity metric of normalized difference
nphenoToy sample metadata table
pathway_GRList of genomic ranges mapped to pathways
pathwayListSample list of pathways
perfCalcComputes variety of predictor evaluation measures based on...
phenoSample metadata table
pheno_fullSubsample of TCGA breast cancer data used for netDx function...
plotEmapCreate EnrichmentMap in Cytoscape to visualize predictive...
plotIntegratedPatientNetworkVisualize integrated patient similarity network based on...
plotPerfPlots various measures of predictor performance for binary...
plotPerf_multiPlots a set of ROC/PR curves with average.
plot_tSNEPlot tSNE
predictPatientLabelsassign patient class when ranked by multiple GM predictors
predResExample output of getPatientRankings, used to call labels for...
pruneNetPrune network by retaining strongest edges
pruneNet_pctXPrune network by retaining strongest edges
pruneNetsPrune interaction networks to keep only the networks and...
randAlphanumStringGenerate random alphanumerical string of length 10
readPathwaysParse GMT file and return pathways as list
RR_featureTallyComputes positive and negative calls upon changing stringency...
runFeatureSelectionRun GeneMANIA cross-validation with a provided subset of...
runQueryRun a query
setupFeatureDBsetup database of features for feature selection
silhToy network.
sim.eucscaleSimilarity method. Euclidean distance followed by exponential...
sim.pearscalevarious similarity functions Similarity function: Pearson...
simpleCapsimple capitalization
smoothMutations_LabelPropThis function applies the random walk with restart...
sparsify2cleaner sparsification routine
sparsify3cleaner sparsification routine - faster, matrix-based version
splitTestTrainSplit samples into train/test
splitTestTrain_resamplingAssign train/test labels over several resamplings of the...
thresholdSmoothedMutationsApply discretization to the matrix resulted from the...
updateNetsSynchronize patient set in sample table and network table.
writeNetsSIFwrite patient networks in Cytoscape's .sif format
writeQueryBatchFileWrite batch.txt file required to create GeneMANIA database
writeQueryFileWrapper to write GeneMANIA query file
writeWeightedNetsWrite an integrated similarity network consisting of selected...
xprExample expression matrix
netDx documentation built on Dec. 11, 2020, 2:01 a.m.