Package org.snpeff.geneSets
Class GeneSetsRanked
- java.lang.Object
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- org.snpeff.geneSets.GeneSets
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- org.snpeff.geneSets.GeneSetsRanked
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Iterable<GeneSet>
public class GeneSetsRanked extends GeneSets
A collection of GeneSets Genes are ranked (usually by 'value')- Author:
- Pablo Cingolani
- See Also:
- Serialized Form
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Field Summary
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Fields inherited from class org.snpeff.geneSets.GeneSets
debug, LOG2, PRINT_SOMETHING_TIME
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Constructor Summary
Constructors Constructor Description GeneSetsRanked()
Default constructorGeneSetsRanked(java.lang.String msigDb)
GeneSetsRanked(GeneSets geneSets)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
add(java.lang.String gene, int rank)
Add a 'ranked' gene (to every corresponding GeneSet in this collection)void
checkInterestingGenes(java.util.Set<java.lang.String> intGenes)
Checks that every symboolID is in the set (as 'interesting' genes)int
getMaxRank()
Get maximum rankint
getRank(java.lang.String gene)
Get gene's rankjava.util.HashMap<java.lang.String,java.lang.Integer>
getRankByGene()
Get geneId <-> Rank mappingint
getRankedSetsCount()
How many gene sets have ranked genes (i.e.boolean
isRanked()
boolean
isRanked(java.lang.String geneName)
protected boolean
isUsed(java.lang.String geneName)
protected boolean
isUsed(GeneSet gs)
Is this gene set used? I.e.java.util.List<java.lang.String>
loadExperimentalValues(java.lang.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
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Constructor Detail
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GeneSetsRanked
public GeneSetsRanked()
Default constructor
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GeneSetsRanked
public GeneSetsRanked(GeneSets geneSets)
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GeneSetsRanked
public GeneSetsRanked(java.lang.String msigDb)
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Method Detail
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add
public boolean add(java.lang.String gene, int rank)
Add a 'ranked' gene (to every corresponding GeneSet in this collection)- Parameters:
gene
- : symbol's IDrank
- : symbol's rank
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checkInterestingGenes
public void checkInterestingGenes(java.util.Set<java.lang.String> intGenes)
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
public int getRank(java.lang.String gene)
Get gene's rank- Parameters:
gene
-- Returns:
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getRankByGene
public java.util.HashMap<java.lang.String,java.lang.Integer> getRankByGene()
Get geneId <-> 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(java.lang.String geneName)
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isUsed
protected boolean isUsed(GeneSet gs)
Is this gene set used? I.e. is there at least one gene 'used'? (e.g. interesting or ranked)
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loadExperimentalValues
public java.util.List<java.lang.String> loadExperimentalValues(java.lang.String fileName, boolean maskException)
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
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