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Functions84 in github.com/califano-lab/ARACNe-AP

⨍ Functions 84◇ Types & classes 15
↓ 10 callersMethodsort
(double[] exp, String[] _gene, boolean _desc)
common/Sorter.java:16
↓ 9 callersMethodgetInformation
(double pXY, double pX, double pY)
aracne/MI.java:662
↓ 7 callersMethodrankVector
(double[] inputVector)
common/Methods.java:57
↓ 5 callersMethodcomputeMI
computeMI for DataVectors when data contains NA values Paracne @param vectorX @param vectorY @return
aracne/MI.java:304
↓ 5 callersMethodrank
(Random random)
common/ExpressionMatrix.java:172
↓ 4 callersMethodfitNull
(double[] _x, int _tailLength)
aracne/MI.java:439
↓ 4 callersMethodgetSamples
()
common/ExpressionMatrix.java:289
↓ 4 callersMethodsetSampleNumber
(int sampleNumber)
aracne/MI.java:676
↓ 2 callersMethodbootstrap
(Random random)
common/ExpressionMatrix.java:205
↓ 2 callersMethodgetGenes
()
common/ExpressionMatrix.java:294
↓ 1 callersMethodcalibrateMIThreshold
(int numberOfSamples, int numberOfGenes, double miPvalue, int _seed)
aracne/MI.java:402
↓ 1 callersMethoddpi
( HashMap<String, HashMap<String, Double>> finalNet, int threadNumber )
aracne/DPI.java:14
↓ 1 callersMethoddpi
( HashMap<String, HashMap<String, Double>> finalNet, int threadNumber )
aracne/Aracne.java:323
↓ 1 callersMethodexchange
(int i, int j)
common/Sorter.java:73
↓ 1 callersMethodgeneratePoissonPvalues
(double mean)
aracne/BootstrapConsolidator.java:136
↓ 1 callersMethodgetBootsamples
()
common/ExpressionMatrix.java:249
↓ 1 callersMethodgetFinalNetwork
()
aracne/MI.java:397
↓ 1 callersMethodgetQuadrants
(DataVector x)
common/DataVector.java:28
↓ 1 callersMethodmergeFiles
(File folder)
aracne/BootstrapConsolidator.java:34
↓ 1 callersMethodpoisson
(double mean, int value)
common/Stats.java:14
↓ 1 callersMethodprintOrderedMIdistribution
()
aracne/MI.java:34
↓ 1 callersMethodquicksort
(int low, int high)
common/Sorter.java:45
↓ 1 callersMethodreadGeneSet
Method to read a gene list
common/DataParser.java:52
↓ 1 callersMethodreadValue
Method to read a file with a single number @throws IOException
common/DataParser.java:33
↓ 1 callersMethodreverse
(short[] shortA)
common/Methods.java:111
↓ 1 callersMethodrunAracne
( File expressionFile1, File expressionFile2, File transcriptionFactorsFile, File outputFolder
aracne/Aracne.java:184
↓ 1 callersMethodrunConsolidate
(File outputFolder, boolean nobonferroni, Double consolidatePvalue)
aracne/Aracne.java:302
↓ 1 callersMethodrunThreshold
(File _expressionFile, File _outputFolder, double miPvalue, int seed)
aracne/Aracne.java:156
↓ 1 callersMethodsetMI
(String _tf, String _gene, double _mi)
aracne/MI.java:193
↓ 1 callersMethodsetMI
(String _tf, String _gene, double _mi)
aracne/MI.java:292
↓ 1 callersMethodshuffleArray
(short[] array, Random random)
common/Methods.java:132
↓ 1 callersMethodwriteFinal
(File finalDPIfile, HashMap<String, HashSet<String>> removedEdges, HashMap<String, HashMap<String, Double>> fi
aracne/Aracne.java:332
↓ 1 callersMethodwriteSignificant
(String outFile, double poissonPvalue)
aracne/BootstrapConsolidator.java:100
↓ 1 callersMethodwriteValue
Method to write a single value into a file
common/DataParser.java:43
MethodBootstrapConsolidator
(boolean nobonferroni)
aracne/BootstrapConsolidator.java:30
MethodDPI
()
aracne/DPI.java:10
MethodDPIThread
(int _i, String[] _tfs, HashMap<String, HashMap<String, Double>> _finalNet, HashMap<String, HashMap<String, Do
aracne/DPI.java:89
MethodDataMatrix
(HashMap<String, DataVector> data, ArrayList<String> genes, ArrayList<String> samples)
common/DataMatrix.java:22
MethodDataVector
(boolean [] NAs, double[] values, String geneName)
common/DataVector.java:12
MethodExpressionMatrix
(double[][] data, ArrayList<String> genes, ArrayList<String> samples)
common/ExpressionMatrix.java:23
MethodMI
( HashMap<String, short[]> rankData1, HashMap<String, short[]> rankData2, String[] tfList, Dou
aracne/MI.java:118
MethodMIThread
(String[] tfs, String[] genes, HashMap<String, short[]> rd1, HashMap<String, short[]> rd2, double mi, int tfNu
aracne/MI.java:168
MethodMIThreadNA
Instantiates a new MI thread na. @param _tfs the _tfs @param _genes the _genes @param _rd1 the _rd1 @param _mi the _mi @param _tfNumber the _tf numbe
aracne/MI.java:268
Methodaccept
(File dir, String name)
aracne/BootstrapConsolidator.java:36
Methodbootstrap
Method to bootstrap NA containing data
common/DataMatrix.java:107
MethodbootstrapNA
Method to bootstrap NA containing data
common/ExpressionMatrix.java:228
MethodcalibrateMIThresholdNA
(HashMap<String, DataVector> _data, int randomPaircount, double miPvalue, int _seed)
aracne/MI.java:478
Methoddifference
(short[] shortA, short[] shortB)
common/Methods.java:97
MethodgenerateRandomVector
(int length, Random random)
common/Methods.java:121
MethodgetData
()
common/ExpressionMatrix.java:285
MethodgetData
()
common/DataMatrix.java:129
MethodgetGenes
()
common/DataMatrix.java:138
MethodgetGenes
()
common/DataParser.java:24
MethodgetGenes
()
common/Sorter.java:12
MethodgetNotNAsInBoth
(DataVector x)
common/DataVector.java:95
MethodgetNotNAsInFirst
(DataVector x)
common/DataVector.java:120
MethodgetNotNAsInSecond
(DataVector x)
common/DataVector.java:144
MethodgetNotNAvalues
()
common/DataVector.java:76
MethodgetSampleNumber
()
aracne/MI.java:672
MethodgetSamples
()
common/DataMatrix.java:133
MethodgetVaues
()
common/Sorter.java:8
Methodintersect
(short[] shortA, short[] shortB)
common/Methods.java:84
Methodmain
(String[] args)
aracne/MI.java:29
Methodmain
(String[] args)
aracne/Aracne.java:31
Methodmain
(String[] args)
common/Stats.java:8
Methodmean
(short[] input)
common/Methods.java:21
Methodmedian
(short[] input)
aracne/MI.java:680
Methodmedian
(short[] input)
common/Methods.java:14
MethodrankTransform
(HashMap<String, HashMap<String, Double>> inputData, double noise)
common/Normalization.java:10
MethodreadCMIthresholds
Method to read a two columns array from a file @throws IOException
common/DataParser.java:100
MethodreadIntegerArray
Method to read an integer list
common/DataParser.java:126
Methodrun
()
aracne/DPI.java:97
Methodrun
()
aracne/MI.java:177
Methodrun
()
aracne/MI.java:276
MethodselectSamples
(ArrayList<String> common)
common/ExpressionMatrix.java:300
MethodselectSamplesNA
(ArrayList<String> common)
common/ExpressionMatrix.java:319
Methodtail
Method to get the last line of a file
common/DataParser.java:187
MethodtestOnePair
(String[] args)
aracne/MI.java:83
MethodtransposeMatrix
(double [][] m)
common/Methods.java:49
Methodunion
(short[] shortA, short[] shortB)
common/Methods.java:71
MethodwriteArraylist
Method to write an integer list @throws IOException
common/DataParser.java:174
MethodwriteCMIthresholds
Method to write a two columns array into a file If several identical MIs are present, the max CMI will be selected @throws IOException
common/DataParser.java:74
MethodwriteIntegerList
Method to write an integer list @throws IOException
common/DataParser.java:148
MethodwriteStringArray
Method to write a string list @throws IOException
common/DataParser.java:161