.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 |