Class GeneSets

Method Details

• factory

  public static GeneSets factory(GoTerms goTerms)

  Create gene sets form GoTerms

  Parameters:

  goTerms - : GoTerms to use

• add

  public void add(GeneSet geneSet)

  Add a gene set

  Parameters:

  geneSetName -

  geneSet -

• add

  public boolean add(String gene)

  Add a gene and aliases

• add

  public boolean add(String gene, GeneSet geneSet)

  Add a gene and it's corresponding gene set

  Parameters:

  gene -

  geneSet -

  Returns:

• addInteresting

  public boolean addInteresting(String gene)

  Add a symbol as 'interesting' gene (to every corresponding GeneSet in this collection)

• checkInterestingGenes

  public void checkInterestingGenes(Set<String> intGenes)

  Checks that every symboolID is in the set (as 'interesting' genes)

  Parameters:

  intGenes - : A set of interesting genes Throws an exception on error

• copy

  protected void copy(GeneSets geneSets)

  Copy all data from geneSets

  Parameters:

  geneSets -

• disjointSet

  public GeneSet disjointSet(List<GeneSet> geneSetList, int activeSets)

  Produce a GeneSet based on a list of GeneSets and a 'mask'

  Parameters:

  geneSetList - : A list of GeneSets

  activeSets - : An integer (binary mask) that specifies weather a set in the list should be taken into account or not. The operation performed is: Intersection{ GeneSets where mask_bit == 1 } - Union{ GeneSets where mask_bit == 0 } ) where the minus sign '-' is actually a 'set minus' operation. This operation is done for both sets in GeneSet (i.e. genes and interestingGenes)

  Returns:

  A GeneSet

• geneSetsSorted

  public List<GeneSet> geneSetsSorted()

  Iterate through each GeneSet in this GeneSets

• geneSetsSortedSize

  public List<GeneSet> geneSetsSortedSize(boolean reverse)

  Gene sets sorted by size (if same size, sort by name).

  Parameters:

  reverse - : Reverse size sorting (does not affect name sorting)

  Returns:

• getGeneCount

  public int getGeneCount()

  How many genes do we have?

  Returns:

• getGenes

  public Set<String> getGenes()

  Get all genes in this set

  Returns:

• getGeneSet

  public GeneSet getGeneSet(String geneSetName)

  Get a gene set named 'geneSetName'

  Parameters:

  geneSetName -

  Returns:

• getGeneSetCount

  public int getGeneSetCount()

  Get number of gene sets

  Returns:

• getGeneSetsByGene

  public HashSet<GeneSet> getGeneSetsByGene(String gene)

  All gene sets that this gene belongs to

  Parameters:

  gene -

  Returns:

• getGeneSetsByName

  public HashMap<String,GeneSet> getGeneSetsByName()

• getInterestingGenes

  public HashSet<String> getInterestingGenes()

• getInterestingGenesCount

  public int getInterestingGenesCount()

• getLabel

  public String getLabel()

• getValue

  public double getValue(String gene)

  Get experimental value

  Parameters:

  gene -

  Returns:

• getValueByGene

  public HashMap<String,Double> getValueByGene()

• hasGene

  public boolean hasGene(String geneId)

• hasValue

  public boolean hasValue(String gene)

• isInteresting

  public boolean isInteresting(String geneName)

• isRanked

  public boolean isRanked()

• 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)

  Parameters:

  gs -

  Returns:

• isUsed

  protected boolean isUsed(String geneName)

• iterator

  public Iterator<GeneSet> iterator()

  Iterate through each GeneSet in this GeneSets

  Specified by:

  iterator in interface Iterable<GeneSet>

• iteratorSorted

  public Iterator<GeneSet> iteratorSorted()

  Iterate through each GeneSet in this GeneSets

• keySet

  public Set<String> keySet()

• listTopTerms

  public List<GeneSet> listTopTerms(int numberToSelect)

  Select a number of GeneSets

  Parameters:

  numberToSelect -

  Returns:

• loadExperimentalValues

  public List<String> loadExperimentalValues(String fileName, boolean maskException)

  Reads a file with a list of genes and experimental values. Format: "gene \t value \n"

  Parameters:

  fileName -

  Returns:

  A list of genes not found

• loadMSigDb

  public boolean loadMSigDb(String gmtFile, boolean maskException)

  Read an MSigDBfile and add every Gene set (do not add relationships between nodes in DAG)

  Parameters:

  gmtFile -

  geneSetType -

• remove

  public void remove(GeneSet geneSet)

• removeGeneSet

  public void removeGeneSet(String geneSetName)

  Remove a GeneSet

• removeUnusedSets

  public void removeUnusedSets()

  Remove unused gene sets

• reset

  public void reset()

  Reset every 'interesting' gene or ranked gene (on every single GeneSet in this GeneSets)

• saveGseaGeneSets

  public void saveGseaGeneSets(String fileName)

  Save gene sets file for GSEA analysis Format specification: http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29

  Parameters:

  fileName -

• setDoNotAddIfNotInGeneSet

  public void setDoNotAddIfNotInGeneSet(boolean doNotAddIfNotInGeneSet)

• setGeneSetByName

  public void setGeneSetByName(HashMap<String,GeneSet> geneSets)

• setInterestingGenes

  public void setInterestingGenes(HashSet<String> interestingGenesIdSet)

• setValue

  public void setValue(String geneId, double value)

  Set experimental value for this gene

  Parameters:

  geneId -

  value -

• setVerbose

  public void setVerbose(boolean verbose)

• toString

  public String toString()

  Overrides:

  toString in class Object

• values

  public Collection<GeneSet> values()