broad.pda.gene.functionalAnnotation Member List

This is the complete list of members for broad.pda.gene.functionalAnnotation, including all inherited members.

calcAllTermsEnrichment(Collection< Gene > geneSet, LinkedList< Collection< Gene >> randomGeneSets)	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)	broad.pda.gene.functionalAnnotation
functionalAnnotation()	broad.pda.gene.functionalAnnotation
getTermGenes(String goTerm, BEDFileParser ref)	broad.pda.gene.functionalAnnotation
loadGoMap(String gofile, String goformat, int goSizeThreshold)	broad.pda.gene.functionalAnnotation
main(String[] args)	broad.pda.gene.functionalAnnotation	static
parseGoRawFiles(String Ontology, String Annotation, String pid2gid, String nm2pidF, int nmCol, int pidCol, String outf)	broad.pda.gene.functionalAnnotation	static
writeTermsEnrichments(String filename, int sizeThreshold, String str, ArrayList< String > termsSorted)	broad.pda.gene.functionalAnnotation