| avgNormDiff | takes average of normdiff of each row in x |
| buildPredictor | Run nested cross-validation on data |
| buildPredictor_sparseGenetic | Performs feature selection using multiple resamplings of the... |
| callFeatSel | Return feature selected nets based on given criteria |
| callOverallSelectedFeatures | Wrapper to call selected features |
| cleanPathwayName | Clean pathway name so it can be a filename. |
| cnv_GR | CNV locations for breast cancer (subset) |
| cnv_netPass | List of pathway-level feature selection scores |
| cnv_netScores | Vector of pathways that pass class enrichment |
| cnv_patientNetCount | Binary matrix of patient occurrence in networks |
| cnv_pheno | data.frame of patient labels and status for CNV example |
| cnv_TTstatus | list of train/test statuses for CNV example |
| compareShortestPath | compare intra-cluster shortest distance to overall shortest... |
| compileFeatures | Create GeneMANIA database |
| compileFeatureScores | Tally the score of networks through cross-validation |
| confmat | Confusion matrix example |
| confusionMatrix | Make confusion matrix |
| convertProfileToNetworks | Convert profiles to interaction networks before integration |
| countIntType | Counts the number of (+,+) and (+,-) interactions in a single... |
| countIntType_batch | Counts number of (+,+) and (+,-) interactions in a set of... |
| countPatientsInNet | Count number of patients in a network |
| createPSN_MultiData | Wrapper to create custom input features (patient similarity... |
| dataList2List | Convert MultiAssayExperiment object to list and data.frame |
| dot-get_cache | wrapper function for getting BiocFileCache associated with... |
| enrichLabelNets | Score networks based on their edge bias towards (+,+)... |
| featScores | Demo feature-level scores from running feature selection on... |
| fetchPathwayDefinitions | fetch pathway definitions from downloads.baderlab.org |
| genes | Table of gene definitions (small subsample of human genes) |
| getCorrType | Counts the relative correlation of (+,+) and (+,-)(-,-)... |
| getEMapInput | write enrichment map for consensus nets |
| getEMapInput_many | Wrapper to generate multiple EnrichmentMaps (perhaps one per... |
| getEnr | Get ENR for all networks in a specified directory |
| getFeatureScores | Compile network scores into a matrix |
| getFileSep | platform-specific file separator |
| getGMjar_path | download and update GeneMANIA jar file |
| getNetConsensus | compile net score across a set of predictor results |
| getOR | Get relative proportion of patient classes that contribute to... |
| getPatientPredictions | Calculates patient-level classification accuracy across... |
| getPatientRankings | Process GM PRANK files to get the ROC curve for the query |
| getPerformance | performance metrics for model |
| getPSN | get the integrated patient similarity network made of... |
| getRegionOL | Returns overlapping named ranges for input ranges |
| getResults | Compiles performance and selected features for a trained... |
| getSimilarity | Measures of patient similarity |
| makeInputForEnrichmentMap | Wrapper to create input files for Enrichment Map |
| makePSN_NamedMatrix | Create patient networks from full matrix of named... |
| makePSN_RangeSets | Create patient similarity interaction networks based on range... |
| makeQueries | Randomly select patients for queries for feature selection |
| makeSymmetric | Convert a network in source-target-weight format to symmetric... |
| mapNamedRangesToSets | Map named ranges to corresponding set of named ranges |
| matrix_getIJ | Converts matrix index (1 to m*n) to row (m) and column (n)... |
| MB.pheno | Sample metadata table for medulloblastoma dataset. |
| modelres | Sample output of getResults() |
| moveInteractionNets | moves interaction networks when compiling database for sparse... |
| normDiff | Similarity metric of normalized difference |
| npheno | Toy sample metadata table |
| pathway_GR | List of genomic ranges mapped to pathways |
| pathwayList | Sample list of pathways |
| perfCalc | Computes variety of predictor evaluation measures based on... |
| pheno | Sample metadata table |
| pheno_full | Subsample of TCGA breast cancer data used for netDx function... |
| plotEmap | Create EnrichmentMap in Cytoscape to visualize predictive... |
| plotIntegratedPatientNetwork | Visualize integrated patient similarity network based on... |
| plotPerf | Plots various measures of predictor performance for binary... |
| plotPerf_multi | Plots a set of ROC/PR curves with average. |
| predict | predict patient labels |
| predictPatientLabels | assign patient class when ranked by multiple GM predictors |
| predRes | Example output of getPatientRankings, used to call labels for... |
| pruneNet | Prune network by retaining strongest edges |
| pruneNet_pctX | Prune network by retaining strongest edges |
| pruneNets | Prune interaction networks to keep only the networks and... |
| randAlphanumString | Generate random alphanumerical string of length 10 |
| readPathways | Parse GMT file and return pathways as list |
| replacePattern | Replace pattern in all files in dir |
| RR_featureTally | Computes positive and negative calls upon changing stringency... |
| runFeatureSelection | Run GeneMANIA cross-validation with a provided subset of... |
| runQuery | Run a query |
| setupFeatureDB | setup database of features for feature selection |
| silh | Toy network. |
| sim.eucscale | Similarity method. Euclidean distance followed by exponential... |
| sim.pearscale | various similarity functions Similarity function: Pearson... |
| simpleCap | simple capitalization |
| smoothMutations_LabelProp | This function applies the random walk with restart... |
| sparsify2 | cleaner sparsification routine |
| sparsify3 | cleaner sparsification routine - faster, matrix-based version |
| splitTestTrain | Split samples into train/test |
| splitTestTrain_resampling | Assign train/test labels over several resamplings of the... |
| thresholdSmoothedMutations | Apply discretization to the matrix resulted from the... |
| toymodel | Example model returned by a buildPredictor() call. |
| tSNEPlotter | Plot tSNE |
| updateNets | Synchronize patient set in sample table and network table. |
| writeNetsSIF | write patient networks in Cytoscape's .sif format |
| writeQueryBatchFile | Write batch.txt file required to create GeneMANIA database |
| writeQueryFile | Wrapper to write GeneMANIA query file |
| writeWeightedNets | Write an integrated similarity network consisting of selected... |
| xpr | Example expression matrix |
