.get_cache              wrapper function for getting BiocFileCache
                        associated with netDx package
MB.pheno                Sample metadata table for medulloblastoma
                        dataset.
RR_featureTally         Computes positive and negative calls upon
                        changing stringency of feature selected
                        networks (binary networks only)
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 data
callFeatSel             Return feature selected nets based on given
                        criteria
cleanPathwayName        Clean pathway name so it can be a filename.
cnv_GR                  CNV locations for breast cancer (subset)
cnv_TTstatus            list of train/test statuses for CNV example
cnv_netPass             Vector of pathways that pass class enrichment
cnv_netScores           List of pathway-level feature selection scores
cnv_patientNetCount     Binary matrix of patient occurrence in networks
cnv_pheno               data.frame of patient labels and status for CNV
                        example
compareShortestPath     compare intra-cluster shortest distance to
                        overall shortest distance of the network
compileFeatureScores    Tally the score of networks through
                        cross-validation
compileFeatures         Create GeneMANIA database
confmat                 Confusion matrix example
convertProfileToNetworks
                        Convert profiles to interaction networks before
                        integration
countIntType            Counts the number of (+,+) and (+,-)
                        interactions in a single network
countIntType_batch      Counts number of (+,+) and (+,-) interactions
                        in a set of networks
countPatientsInNet      Count number of patients in a network
createPSN_MultiData     Wrapper to create custom input features
                        (patient similarity networks)
dataList2List           Convert MultiAssayExperiment object to list and
                        data.frame
enrichLabelNets         Score networks based on their edge bias towards
                        (+,+) interactions
featScores              Demo feature-level scores from running feature
                        selection on two-class problem
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
                        (+,-)(-,-) interactions
getEMapInput            write enrichment map for consensus nets
getEMapInput_many       Wrapper to generate multiple EnrichmentMaps
                        (perhaps one per class)
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 a set of networks
getPatientPredictions   Calculates patient-level classification
                        accuracy across train/test splits
getPatientRankings      Process GM PRANK files to get the ROC curve for
                        the query
getRegionOL             Returns overlapping named ranges for input
                        ranges
getSimilarity           Measures of patient similarity
makePSN_NamedMatrix     Create patient networks from full matrix of
                        named measurements
makePSN_RangeSets       Create patient similarity interaction networks
                        based on range sets
makeQueries             Randomly select patients for queries for
                        feature selection
makeSymmetric           Convert a network in source-target-weight
                        format to symmetric matrix
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) number
moveInteractionNets     moves interaction networks when compiling
                        database for sparse genetic workflow
normDiff                Similarity metric of normalized difference
npheno                  Toy sample metadata table
pathwayList             Sample list of pathways
pathway_GR              List of genomic ranges mapped to pathways
perfCalc                Computes variety of predictor evaluation
                        measures based on the confusion matrix
pheno                   Sample metadata table
pheno_full              Subsample of TCGA breast cancer data used for
                        netDx function examples
plotEmap                Create EnrichmentMap in Cytoscape to visualize
                        predictive pathways
plotIntegratedPatientNetwork
                        Visualize integrated patient similarity network
                        based on selected features
plotPerf                Plots various measures of predictor performance
                        for binary classifiers
plotPerf_multi          Plots a set of ROC/PR curves with average.
plot_tSNE               Plot tSNE
predRes                 Example output of getPatientRankings, used to
                        call labels for test patients.
predictPatientLabels    assign patient class when ranked by multiple GM
                        predictors
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 patients requested
randAlphanumString      Generate random alphanumerical string of length
                        10
readPathways            Parse GMT file and return pathways as list
runFeatureSelection     Run GeneMANIA cross-validation with a provided
                        subset of networks
runQuery                Run a query
setupFeatureDB          setup database of features for feature
                        selection
silh                    Toy network.
sim.eucscale            Similarity method. Euclidean distance followed
                        by exponential scaling
sim.pearscale           various similarity functions Similarity
                        function: Pearson correlation followed by
                        exponential scaling
simpleCap               simple capitalization
smoothMutations_LabelProp
                        This function applies the random walk with
                        restart propagation algorithm to a matrix of
                        patients profiles
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 data.
thresholdSmoothedMutations
                        Apply discretization to the matrix resulted
                        from the propagation on the sparse patient
                        matrix
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 networks.
xpr                     Example expression matrix
