Collaboration diagram for broad.pda.gene.functionalAnnotation:

Public Member Functions
	functionalAnnotation ()

void	loadGoMap (String gofile, String goformat, int goSizeThreshold) throws IOException

void	calcAllTermsEnrichment (Collection< Gene > geneSet, LinkedList< Collection< Gene >> randomGeneSets)

void	calcTermEnrichment (String term, HashMap< String, String > geneSet, LinkedList< HashMap< String, String >> randomSets, Double[] permPval, Double[] fischerExact, Integer[] numOverlap, LinkedList< Double > randomFischerExact, LinkedList< Integer > randomOverlap)

void	writeTermsEnrichments (String filename, int sizeThreshold, String str, ArrayList< String > termsSorted) throws IOException

Set< Gene >	getTermGenes (String goTerm, BEDFileParser ref)

Static Public Member Functions
static void	parseGoRawFiles (String Ontology, String Annotation, String pid2gid, String nm2pidF, int nmCol, int pidCol, String outf) throws IOException

static void	main (String[] args) throws Exception

Constructor & Destructor Documentation

broad.pda.gene.functionalAnnotation.functionalAnnotation ( )

Here is the caller graph for this function:

Member Function Documentation

void broad.pda.gene.functionalAnnotation.calcAllTermsEnrichment	(	Collection< Gene >	geneSet,
		LinkedList< Collection< Gene >>	randomGeneSets
	)

Here is the call graph for this function:

void broad.pda.gene.functionalAnnotation.calcTermEnrichment	(	String	term,
		HashMap< String, String >	geneSet,
		LinkedList< HashMap< String, String >>	randomSets,
		Double[]	permPval,
		Double[]	fischerExact,
		Integer[]	numOverlap,
		LinkedList< Double >	randomFischerExact,
		LinkedList< Integer >	randomOverlap
	)

Here is the caller graph for this function:

Set<Gene> broad.pda.gene.functionalAnnotation.getTermGenes	(	String	goTerm,
		BEDFileParser	ref
	)

void broad.pda.gene.functionalAnnotation.loadGoMap	(	String	gofile,
		String	goformat,
		int	goSizeThreshold
	)		throws IOException

static void broad.pda.gene.functionalAnnotation.main ( String[] args ) throws Exception

static

Here is the call graph for this function:

static void broad.pda.gene.functionalAnnotation.parseGoRawFiles	(	String	Ontology,
		String	Annotation,
		String	pid2gid,
		String	nm2pidF,
		int	nmCol,
		int	pidCol,
		String	outf
	)		throws IOException

static

Here is the caller graph for this function:

void broad.pda.gene.functionalAnnotation.writeTermsEnrichments	(	String	filename,
		int	sizeThreshold,
		String	str,
		ArrayList< String >	termsSorted
	)		throws IOException

The documentation for this class was generated from the following file: