Package org.monarchinitiative.lirical.background.backgroundfrequency

Class GenicIntoleranceCalculator

java.lang.Object

org.monarchinitiative.lirical.background.backgroundfrequency.GenicIntoleranceCalculator

public class GenicIntoleranceCalculator
extends Object

This class calculates the relative proportions of variants assessed as having a certain degree of pathogenicity by Exomiser. We examine all of the variants and place them into two pathogenicity bins: predicted benign (0-0.8) and predicted pathogenic (0.8-1.0). We then calculate the sum of all predicted pathogenic variant frequencies using the population background from the Exomiser database (gnomAD, TOPMed, others, but filtering out variants that are listed in ClinVar).

Author:

Jules Jacobsen, Peter Robinson

Constructor Summary

Constructors

Constructor	Description
GenicIntoleranceCalculator(org.monarchinitiative.svart.assembly.GenomicAssembly assembly, FunctionalVariantAnnotator variantAnnotator, org.h2.mvstore.MVStore alleleStore, boolean doClinvar)

Method Summary

Modifier and Type	Method	Description
void	run(Path outputFileName)	This function inputs the data from the MV store, bins each variant into one of four categories, normalizes the frequencies, and writes the results to a file that can be used elsewhere.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

GenicIntoleranceCalculator

public GenicIntoleranceCalculator(org.monarchinitiative.svart.assembly.GenomicAssembly assembly,
 FunctionalVariantAnnotator variantAnnotator,
 org.h2.mvstore.MVStore alleleStore,
 boolean doClinvar)

Parameters:

assembly -

variantAnnotator - Object to annotate an arbitrary variant

alleleStore - Exomiser data resource

doClinvar - flag that if true will cause the analysis to calculate the distribution of Clinvar pathogenicity scores

Method Details

run

public void run(Path outputFileName)

This function inputs the data from the MV store, bins each variant into one of four categories, normalizes the frequencies, and writes the results to a file that can be used elsewhere.