public class SetOverlapAnalysis
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
java.util.Vector<java.lang.String> |
allproteins |
java.util.Vector<java.util.Vector<java.lang.String>> |
lists |
java.util.Vector<java.lang.String> |
setnames |
java.util.Vector<java.util.HashSet<java.lang.String>> |
sets |
Constructor and Description |
---|
SetOverlapAnalysis() |
Modifier and Type | Method and Description |
---|---|
java.util.Vector<OmegaScoreData> |
analyzeHitFrequency(java.util.Vector<java.util.Vector<java.lang.String>> hitSet) |
java.util.Vector<java.lang.String> |
calcIntersectionOfSets(java.util.HashSet<java.lang.String> set1,
java.util.HashSet<java.lang.String> set2) |
java.util.Vector<java.lang.String> |
calcUnionOfSets() |
static void |
convertSetofGMTsToTable(java.util.Vector<java.lang.String> gmts) |
java.util.Vector<java.lang.String> |
convertSetToVector(java.util.HashSet<java.lang.String> set) |
void |
convertTableSetToGMT(java.lang.String fnSetTable,
java.lang.String fnSetGMT,
int maxSize) |
static void |
convertXGMMLtoGMT(java.lang.String xgmmlFileName,
java.lang.String gmtFileName,
boolean splitIntoPairs) |
java.util.Vector<java.lang.Integer> |
countOccurenciesInSets(java.util.Vector<java.lang.String> list,
java.util.Vector<java.lang.Float> percentages) |
void |
createGMTFromOCSANAOutput(java.lang.String fn) |
void |
expandSetsOfLists_ExpandSets(java.lang.String setGMT,
java.lang.String expansionSetGMT,
java.lang.String fn) |
void |
expandSetsOfLists_SplitSets(java.lang.String setGMT,
java.lang.String expansionSetGMT,
java.lang.String fn) |
void |
findMinimalHittingSet(int maxSetSize,
java.lang.String fileNamePreifix) |
void |
generateAllCombinations(java.util.Vector<java.lang.String> currentSet,
java.util.Vector<java.util.Vector<java.lang.String>> setofsets,
java.util.Vector<java.lang.String> names,
java.util.Vector<java.util.HashSet<java.lang.String>> sets,
java.lang.String name,
int number) |
static void |
generateAllPairwiseGMT(java.lang.String gmtFile,
java.lang.String newFile) |
void |
generateSetsFromRankedLists(int numberOfTopRanked) |
Graph |
getBiPartiteSetConnectionGraph(java.lang.String gmtSets,
java.lang.String gmtConnectors,
int numberOfPermutations) |
static float |
getConnectionGraphCoverageScore(Graph graph) |
java.util.Vector<java.lang.String> |
getListOfSets(java.lang.String node) |
int |
getMaximumSetSize() |
java.util.Vector<java.lang.String> |
getNamesOfGivenOccurence(int occ) |
int |
intersect2ListsOfSets(SetOverlapAnalysis so1,
SetOverlapAnalysis so2) |
int |
intersect2ListsOfSets(java.lang.String gmt1,
java.lang.String gmt2) |
int |
intersect2ListsOfSets(java.lang.String gmt1,
java.lang.String gmt2,
int numberOfReshuffles,
int numbeOfPermutationsForPValue) |
int |
listSetsIncludingSet(java.util.HashSet<java.lang.String> subset) |
void |
listSetsIncludingSet(java.lang.String fileName,
java.util.HashSet<java.lang.String> subset) |
void |
listSetsIncludingSet(java.lang.String fileName,
java.lang.String[] subset) |
void |
LoadNewOrderedList(java.lang.String fn) |
static java.util.Vector<java.lang.String> |
loadRandkedGeneList(java.lang.String fileName) |
void |
LoadSetsFromGMT(java.lang.String fn) |
void |
loadSetsFromTable(java.lang.String fileName) |
static void |
main(java.lang.String[] args) |
void |
makeGMTOfReactionRegulators(java.lang.String prefix,
Graph reactionGraph,
java.lang.String[] typesOfRegulations) |
void |
printSetIntersections(java.lang.String filename) |
static void |
printSetIntersectionsInFolder(java.lang.String folder) |
void |
printSetSizes() |
void |
reshuffleSets(int numberOfPermutations,
boolean conserveSizes) |
void |
saveSetsAsGMT(java.lang.String fnSetGMT,
int maxSize) |
public java.util.Vector<java.util.Vector<java.lang.String>> lists
public java.util.Vector<java.util.HashSet<java.lang.String>> sets
public java.util.Vector<java.lang.String> setnames
public java.util.Vector<java.lang.String> allproteins
public static void main(java.lang.String[] args)
args
- public void LoadNewOrderedList(java.lang.String fn)
public void LoadSetsFromGMT(java.lang.String fn)
public static java.util.Vector<java.lang.String> loadRandkedGeneList(java.lang.String fileName)
public void generateSetsFromRankedLists(int numberOfTopRanked)
public java.util.Vector<java.lang.String> calcUnionOfSets()
public java.util.Vector<java.lang.String> calcIntersectionOfSets(java.util.HashSet<java.lang.String> set1, java.util.HashSet<java.lang.String> set2)
public java.util.Vector<java.lang.Integer> countOccurenciesInSets(java.util.Vector<java.lang.String> list, java.util.Vector<java.lang.Float> percentages)
public java.util.Vector<java.lang.String> getNamesOfGivenOccurence(int occ)
public void printSetSizes()
public void printSetIntersections(java.lang.String filename) throws java.lang.Exception
java.lang.Exception
public static void printSetIntersectionsInFolder(java.lang.String folder) throws java.lang.Exception
java.lang.Exception
public void findMinimalHittingSet(int maxSetSize, java.lang.String fileNamePreifix) throws java.lang.Exception
java.lang.Exception
public java.util.Vector<java.lang.String> getListOfSets(java.lang.String node)
public java.util.Vector<OmegaScoreData> analyzeHitFrequency(java.util.Vector<java.util.Vector<java.lang.String>> hitSet)
public void createGMTFromOCSANAOutput(java.lang.String fn) throws java.lang.Exception
java.lang.Exception
public void makeGMTOfReactionRegulators(java.lang.String prefix, Graph reactionGraph, java.lang.String[] typesOfRegulations) throws java.lang.Exception
java.lang.Exception
public void listSetsIncludingSet(java.lang.String fileName, java.lang.String[] subset)
public void listSetsIncludingSet(java.lang.String fileName, java.util.HashSet<java.lang.String> subset)
public int listSetsIncludingSet(java.util.HashSet<java.lang.String> subset)
public int getMaximumSetSize()
public java.util.Vector<java.lang.String> convertSetToVector(java.util.HashSet<java.lang.String> set)
public void loadSetsFromTable(java.lang.String fileName)
public void convertTableSetToGMT(java.lang.String fnSetTable, java.lang.String fnSetGMT, int maxSize) throws java.lang.Exception
java.lang.Exception
public void saveSetsAsGMT(java.lang.String fnSetGMT, int maxSize) throws java.lang.Exception
java.lang.Exception
public static void convertSetofGMTsToTable(java.util.Vector<java.lang.String> gmts)
public void expandSetsOfLists_ExpandSets(java.lang.String setGMT, java.lang.String expansionSetGMT, java.lang.String fn) throws java.lang.Exception
java.lang.Exception
public void expandSetsOfLists_SplitSets(java.lang.String setGMT, java.lang.String expansionSetGMT, java.lang.String fn) throws java.lang.Exception
java.lang.Exception
public void generateAllCombinations(java.util.Vector<java.lang.String> currentSet, java.util.Vector<java.util.Vector<java.lang.String>> setofsets, java.util.Vector<java.lang.String> names, java.util.Vector<java.util.HashSet<java.lang.String>> sets, java.lang.String name, int number)
public static void convertXGMMLtoGMT(java.lang.String xgmmlFileName, java.lang.String gmtFileName, boolean splitIntoPairs) throws java.lang.Exception
java.lang.Exception
public int intersect2ListsOfSets(java.lang.String gmt1, java.lang.String gmt2)
public int intersect2ListsOfSets(java.lang.String gmt1, java.lang.String gmt2, int numberOfReshuffles, int numbeOfPermutationsForPValue)
public int intersect2ListsOfSets(SetOverlapAnalysis so1, SetOverlapAnalysis so2)
public void reshuffleSets(int numberOfPermutations, boolean conserveSizes)
public Graph getBiPartiteSetConnectionGraph(java.lang.String gmtSets, java.lang.String gmtConnectors, int numberOfPermutations) throws java.lang.Exception
java.lang.Exception
public static float getConnectionGraphCoverageScore(Graph graph)
public static void generateAllPairwiseGMT(java.lang.String gmtFile, java.lang.String newFile) throws java.lang.Exception
java.lang.Exception