Package org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency

Class FrequencyData

java.lang.Object
org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
public class FrequencyData extends Object
Frequency data for the variant from the Thousand Genomes, the Exome Server Project and Broad ExAC datasets.

Note that the frequency data are expressed as percentages.

Author:
Jules Jacobsen

  • Method Details

    • of

      public static FrequencyData of(String rsId, Collection<Frequency> frequencies)

    • of

      public static FrequencyData of(Collection<Frequency> frequencies)

    • of

      public static FrequencyData of(String rsId, Frequency frequency)

    • of

      public static FrequencyData of(String rsId, Frequency... frequency)

    • of

      public static FrequencyData of(Frequency... frequency)

    • of

      public static FrequencyData of(Frequency frequency)

    • empty

      public static FrequencyData empty()

    • getRsId

      public String getRsId()

    • getFrequencyForSource

      public Frequency getFrequencyForSource(FrequencySource source)

    • isRepresentedInDatabase

      public boolean isRepresentedInDatabase()
      Returns:
      true if this variant is at all represented in dbSNP or ESP data, regardless of frequency. That is, if the variant has an RS id in dbSNP or any frequency data at all, return true, otherwise false.

    • hasDbSnpData

      public boolean hasDbSnpData()

    • hasDbSnpRsID

      public boolean hasDbSnpRsID()

    • hasEspData

      public boolean hasEspData()

    • hasExacData

      public boolean hasExacData()

    • hasKnownFrequency

      public boolean hasKnownFrequency()

    • hasFrequencyOverPercentageValue

      public boolean hasFrequencyOverPercentageValue(float maxFreq)
      This function tests whether or not this FrequencyData object contains a Frequency object which has a frequency greater than the maximum frequency provided. This method does not check any ranges so it is advised that the user checks the frequency type in advance of calling this method. By default exomiser expresses the frequencies as a percentage value.
      Parameters:
      maxFreq - the maximum frequency threshold against which the Frequency objects are tested
      Returns:
      true if the object contains a Frequency over the provided percentage value, otherwise returns false.
      Since:
      10.1.0

    • getKnownFrequencies

      public List<Frequency> getKnownFrequencies()
      Returns a list of Frequency objects. If there is no known frequency data then an empty list will be returned. This method will return a mutable copy of the underlying data.
      Returns:
      a mutable copy of the Frequency data

    • getMaxFreq

      public float getMaxFreq()
      Returns a the maximum frequency - if there are no known frequencies/ no frequency data it will return 0.
      Returns:

    • getScore

      public float getScore()
      Returns:
      returns a numerical value that is closer to one, the rarer the variant is. If a variant is not entered in any of the data sources, it returns one (highest score). Otherwise, it identifies the maximum MAF in any of the databases, and returns a score that depends on the MAF. Note that the frequency is expressed as a percentage.

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object