Uses of Class
org.snpeff.geneSets.GeneSet
Packages that use GeneSet
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Uses of GeneSet in org.snpeff.geneSets
Methods in org.snpeff.geneSets that return GeneSetModifier and TypeMethodDescriptionGeneSets.disjointSet(List<GeneSet> geneSetList, int activeSets) Produce a GeneSet based on a list of GeneSets and a 'mask'GeneSets.getGeneSet(String geneSetName) Get a gene set named 'geneSetName'Result.getLatestGeneSet()Methods in org.snpeff.geneSets that return types with arguments of type GeneSetModifier and TypeMethodDescriptionGeneSets.geneSetsSorted()Iterate through each GeneSet in this GeneSetsGeneSets.geneSetsSortedSize(boolean reverse) Gene sets sorted by size (if same size, sort by name).Result.getGeneSets()GeneSets.getGeneSetsByGene(String gene) All gene sets that this gene belongs toGeneSets.getGeneSetsByName()GeneSets.iterator()Iterate through each GeneSet in this GeneSetsGeneSets.iteratorSorted()Iterate through each GeneSet in this GeneSetsGeneSets.listTopTerms(int numberToSelect) Select a number of GeneSetsGeneSets.values()Methods in org.snpeff.geneSets with parameters of type GeneSetModifier and TypeMethodDescriptionbooleanAdd a gene and it's corresponding gene setvoidAdd a gene setintComparable interface (to order terms)intGeneSet.countOverlap(GeneSet gs) COunt how many genes are in both GeneSetsvoidGeneSet.intersection(GeneSet geneSet) Intersects this term with 'geneSet' (intersects 'geneSet' and 'interestingGeneSet').protected booleanIs this gene set used? I.e.protected booleanIs this gene set used? I.e.voidvoidPerform a 'set minus' between this term and 'geneSet' (set minus for 'geneSet' and 'interestingGeneSet').voidUnion this term with 'geneSet' (union for 'geneSet' and 'interestingGeneSet').Method parameters in org.snpeff.geneSets with type arguments of type GeneSetModifier and TypeMethodDescriptionGeneSets.disjointSet(List<GeneSet> geneSetList, int activeSets) Produce a GeneSet based on a list of GeneSets and a 'mask'voidSer a new list and pvaluevoidGeneSets.setGeneSetByName(HashMap<String, GeneSet> geneSets) voidResult.setGeneSets(List<GeneSet> newGeneSets) Assign geneSetsConstructors in org.snpeff.geneSets with parameters of type GeneSetModifierConstructorDescriptionConstructor parameters in org.snpeff.geneSets with type arguments of type GeneSet