| Methods in baseCode.bio.geneset with parameters of type GeneAnnotations |
static double |
GeneSetMapTools.meanGeneSetSize(GeneAnnotations ga,
boolean countEmpty)
|
static double |
GeneSetMapTools.meanSetsPerGene(GeneAnnotations ga,
boolean countEmpty)
|
static hep.aida.IHistogram1D |
GeneSetMapTools.geneSetSizeDistribution(GeneAnnotations ga,
int numBins,
int minSize,
int maxSize)
|
static void |
GeneSetMapTools.removeAspect(GeneAnnotations ga,
GONames gon,
StatusViewer messenger,
java.lang.String aspect)
|
static void |
GeneSetMapTools.removeBySize(GeneAnnotations ga,
StatusViewer messenger,
int minClassSize,
int maxClassSize)
Remove gene sets that don't meet certain criteria. |
static void |
GeneSetMapTools.ignoreSimilar(double fractionSameThreshold,
GeneAnnotations ga,
StatusViewer messenger,
int maxClassSize,
int minClassSize,
double bigClassPenalty)
Remove classes which are too similar to some other class. |
static void |
GeneSetMapTools.collapseGeneSets(GeneAnnotations geneData,
StatusViewer messenger)
Identify classes which are absoluely identical to others. |