A B C D E F G M N P R S T U W X misc
allowedSims | built-in similarity functions |
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 |
callOverallSelectedFeatures | Wrapper to call selected features |
checkMakeNetFuncSims | internal test function to check validity of makeNetFunc and sims |
checkSimValid | checks if provided similarity functions are valid. Returns error if not |
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 |
confusionMatrix | Make confusion matrix |
convertProfileToNetworks | Convert profiles to interaction networks before integration |
convertToMAE | Wrapper that converts an input list into a MultiAssayExperiment object |
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 |
createNetFuncFromSimList | Create PSN from provided similarities |
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 |
getPerformance | performance metrics for model |
getPSN | get the integrated patient similarity network made of selected features |
getRegionOL | Returns overlapping named ranges for input ranges |
getResults | Compiles performance and selected features for a trained model. |
getSimilarity | Measures of patient similarity |
makeInputForEnrichmentMap | Wrapper to create input files for Enrichment Map |
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. |
modelres | Sample output of getResults() |
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. |
predict | predict patient labels |
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 |
psn__builtIn | make PSN for built-in similarity functions |
psn__corr | wrapper for PSNs using Pearson correlation |
psn__custom | make PSN for custom similarity functions |
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 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. |
subsampleValidationData | Subsample a hold-out set from a larger patient dataset |
thresholdSmoothedMutations | Apply discretization to the matrix resulted from the propagation on the sparse patient matrix |
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 networks. |
xpr | Example expression matrix |
.get_cache | wrapper function for getting BiocFileCache associated with netDx package |