Network-based patient classifier


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Documentation for package ‘netDx’ version 1.2.2

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.get_cache wrapper function for getting BiocFileCache associated with netDx package
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_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
cnv_TTstatus list of train/test statuses for CNV example
compareShortestPath compare intra-cluster shortest distance to overall shortest distance of the network
compileFeatures Create GeneMANIA database
compileFeatureScores Tally the score of networks through cross-validation
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
MB.pheno Sample metadata table for medulloblastoma dataset.
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
predictPatientLabels assign patient class when ranked by multiple GM predictors
predRes Example output of getPatientRankings, used to call labels for test patients.
pruneNet Prune network by retaining strongest edges
pruneNets Prune interaction networks to keep only the networks and patients requested
pruneNet_pctX Prune network by retaining strongest edges
randAlphanumString Generate random alphanumerical string of length 10
readPathways Parse GMT file and return pathways as list
RR_featureTally Computes positive and negative calls upon changing stringency of feature selected networks (binary networks only)
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