broad.core.overlaputils.GeneSetIntersect Member List

This is the complete list of members for broad.core.overlaputils.GeneSetIntersect, including all inherited members.

countOverlappers(Map< String, Collection< Gene >> regionsToCount, Map< String, Collection< Gene >> regionsToOverlapWith)	broad.core.overlaputils.GeneSetIntersect	static
countOverlappers(Map< String, Collection< Gene >> regionsToCount, Map< String, Collection< Gene >> regionsToOverlapWith, Map< String, Collection< Gene >> excludeSet)	broad.core.overlaputils.GeneSetIntersect	static
getOverlap(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)	broad.core.overlaputils.GeneSetIntersect	static
getOverlap(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, boolean verbose)	broad.core.overlaputils.GeneSetIntersect	static
getOverlap(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet)	broad.core.overlaputils.GeneSetIntersect	static
getOverlap(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet, boolean verbose)	broad.core.overlaputils.GeneSetIntersect	static
getOverlapWithRandomizedPositions(Map< String, Collection< Gene >> regions, Map< String, Collection< Gene >> intersectGenes)	broad.core.overlaputils.GeneSetIntersect	static
getOverlapWithRandomizedPositions(Map< String, Collection< Gene >> regions, Map< String, Collection< Gene >> intersectGenes, Map< String, Collection< Gene >> excludeFeatures)	broad.core.overlaputils.GeneSetIntersect	static
main(String[] args)	broad.core.overlaputils.GeneSetIntersect	static
mapGenesToOverlappers(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)	broad.core.overlaputils.GeneSetIntersect	static
numOverlappingBases(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)	broad.core.overlaputils.GeneSetIntersect	static
numOverlappingBases(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet)	broad.core.overlaputils.GeneSetIntersect	static
numOverlappingGenes(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet)	broad.core.overlaputils.GeneSetIntersect	static
numOverlappingGenes(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeGenes)	broad.core.overlaputils.GeneSetIntersect	static
writeGeneralStats(String geneFile, String intersectFile1, String intersectFile2, String excludeFile, String outFile)	broad.core.overlaputils.GeneSetIntersect	static
writeOverlap(String geneFile, String intersectFile, String outFile, boolean randomizePositionsWithinEachGene)	broad.core.overlaputils.GeneSetIntersect	static
writeOverlap(String geneFile, String intersectFile, String excludeFile, String outFile, boolean randomizePositionsWithinEachGene)	broad.core.overlaputils.GeneSetIntersect	static
writeOverlap(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, String outFile, boolean randomizePositionsWithinEachGene)	broad.core.overlaputils.GeneSetIntersect	static
writeOverlap(Map< String, Collection< Gene >> genes, Map< String, Collection< Gene >> intersectSet, Map< String, Collection< Gene >> excludeSet, String outFile, boolean randomizePositionsWithinEachGene)	broad.core.overlaputils.GeneSetIntersect	static