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 TypeMethodDescriptionboolean
Add a gene and it's corresponding gene setvoid
Add a gene setint
Comparable interface (to order terms)int
GeneSet.countOverlap
(GeneSet gs) COunt how many genes are in both GeneSetsvoid
GeneSet.intersection
(GeneSet geneSet) Intersects this term with 'geneSet' (intersects 'geneSet' and 'interestingGeneSet').protected boolean
Is this gene set used? I.e.protected boolean
Is this gene set used? I.e.void
void
Perform a 'set minus' between this term and 'geneSet' (set minus for 'geneSet' and 'interestingGeneSet').void
Union 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'void
Ser a new list and pvaluevoid
GeneSets.setGeneSetByName
(HashMap<String, GeneSet> geneSets) void
Result.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