# Network-based patient classifier

## Documentation for package ‘netDx’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G M N P R S T U W X misc

## -- A --

allowedSims | built-in similarity functions
avgNormDiff | takes average of normdiff of each row in x

## -- B --

buildPredictor | Run nested cross-validation on data
buildPredictor_sparseGenetic | Performs feature selection using multiple resamplings of the data

## -- C --

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)

## -- D --

dataList2List | Convert MultiAssayExperiment object to list and data.frame

## -- E --

enrichLabelNets | Score networks based on their edge bias towards (+,+) interactions

## -- F --

featScores | Demo feature-level scores from running feature selection on two-class problem
fetchPathwayDefinitions | fetch pathway definitions from downloads.baderlab.org

## -- G --

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

## -- M --

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

## -- N --

normDiff | Similarity metric of normalized difference
npheno | Toy sample metadata table

## -- P --

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

## -- R --

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

## -- S --

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

## -- T --

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

## -- U --

updateNets | Synchronize patient set in sample table and network table.

## -- W --

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.

## -- X --

xpr | Example expression matrix

## -- misc --

.get_cache | wrapper function for getting BiocFileCache associated with netDx package