Package org.snpeff.geneSets
Class GeneSetsRanked
java.lang.Object
org.snpeff.geneSets.GeneSets
org.snpeff.geneSets.GeneSetsRanked
- All Implemented Interfaces:
Serializable
,Iterable<GeneSet>
A collection of GeneSets
Genes are ranked (usually by 'value')
- Author:
- Pablo Cingolani
- See Also:
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Field Summary
Fields inherited from class org.snpeff.geneSets.GeneSets
debug, LOG2, PRINT_SOMETHING_TIME
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Constructor Summary
ConstructorsConstructorDescriptionDefault constructorGeneSetsRanked
(String msigDb) GeneSetsRanked
(GeneSets geneSets) -
Method Summary
Modifier and TypeMethodDescriptionboolean
Add a 'ranked' gene (to every corresponding GeneSet in this collection)void
checkInterestingGenes
(Set<String> intGenes) Checks that every symboolID is in the set (as 'interesting' genes)int
Get maximum rankint
Get gene's rankGet geneId invalid input: '<'-> Rank mappingint
How many gene sets have ranked genes (i.e.boolean
isRanked()
boolean
protected boolean
protected boolean
Is this gene set used? I.e.loadExperimentalValues
(String fileName, boolean maskException) Reads a file with a list of genes and experimental values.int
rankByValue
(boolean orderAscending) Rank genes by valuevoid
reset()
Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)Methods inherited from class org.snpeff.geneSets.GeneSets
add, add, add, addInteresting, copy, disjointSet, factory, geneSetsSorted, geneSetsSortedSize, getGeneCount, getGenes, getGeneSet, getGeneSetCount, getGeneSetsByGene, getGeneSetsByName, getInterestingGenes, getInterestingGenesCount, getLabel, getValue, getValueByGene, hasGene, hasValue, isInteresting, iterator, iteratorSorted, keySet, listTopTerms, loadMSigDb, remove, removeGeneSet, removeUnusedSets, saveGseaGeneSets, setDoNotAddIfNotInGeneSet, setGeneSetByName, setInterestingGenes, setValue, setVerbose, toString, values
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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GeneSetsRanked
public GeneSetsRanked()Default constructor -
GeneSetsRanked
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GeneSetsRanked
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Method Details
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add
Add a 'ranked' gene (to every corresponding GeneSet in this collection)- Parameters:
gene
- : symbol's IDrank
- : symbol's rank
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checkInterestingGenes
Checks that every symboolID is in the set (as 'interesting' genes)- Overrides:
checkInterestingGenes
in classGeneSets
- Parameters:
intGenes
- : A set of interesting genes Throws an exception on error
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getMaxRank
public int getMaxRank()Get maximum rank- Returns:
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getRank
Get gene's rank- Parameters:
gene
-- Returns:
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getRankByGene
Get geneId invalid input: '<'-> Rank mapping- Returns:
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getRankedSetsCount
public int getRankedSetsCount()How many gene sets have ranked genes (i.e. rank sum > 0)- Returns:
- Number of gene set such that rankSum > 0
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isRanked
public boolean isRanked() -
isRanked
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isUsed
Is this gene set used? I.e. is there at least one gene 'used'? (e.g. interesting or ranked) -
isUsed
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loadExperimentalValues
Reads a file with a list of genes and experimental values. Format: "gene \t value \n"- Overrides:
loadExperimentalValues
in classGeneSets
- Parameters:
fileName
-- Returns:
- A list of genes not found
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rankByValue
public int rankByValue(boolean orderAscending) Rank genes by value -
reset
public void reset()Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)
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