picard.analysis

Class TheoreticalSensitivity

java.lang.Object

picard.analysis.TheoreticalSensitivity

public class TheoreticalSensitivity
extends java.lang.Object

Created by David Benjamin on 5/13/15.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TheoreticalSensitivity.RouletteWheel

Constructor Summary

Constructors

Constructor and Description
TheoreticalSensitivity()

Method Summary

Modifier and Type	Method and Description
static java.util.List<java.util.ArrayList<java.lang.Double>>	hetAltDepthDistribution(int N)
static double	hetSNPSensitivity(double[] depthDistribution, double[] qualityDistribution, int sampleSize, double logOddsThreshold)
static double	hetSNPSensitivity(double[] depthDistribution, double[] qualityDistribution, int sampleSize, double logOddsThreshold, boolean withLogging)
static double[]	normalizeHistogram(htsjdk.samtools.util.Histogram<java.lang.Integer> histogram)
static java.util.List<java.util.ArrayList<java.lang.Double>>	proportionsAboveThresholds(java.util.List<java.util.ArrayList<java.lang.Integer>> lists, java.util.List<java.lang.Double> thresholds)

Methods inherited from class java.lang.Object

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

Constructor Detail

TheoreticalSensitivity

public TheoreticalSensitivity()

Method Detail

hetSNPSensitivity

public static double hetSNPSensitivity(double[] depthDistribution,
                                       double[] qualityDistribution,
                                       int sampleSize,
                                       double logOddsThreshold)

Parameters:

depthDistribution - the probability of depth n is depthDistribution[n] for n = 0, 1. . . N - 1

qualityDistribution - the probability of quality q is qualityDistribution[q] for q = 0, 1. . . Q

sampleSize - sample size is the number of random sums of quality scores for each m

logOddsThreshold - is the log_10 of the likelihood ratio required to call a SNP, for example 5 if the variant likelihood must be 10^5 times greater

hetSNPSensitivity

public static double hetSNPSensitivity(double[] depthDistribution,
                                       double[] qualityDistribution,
                                       int sampleSize,
                                       double logOddsThreshold,
                                       boolean withLogging)

Parameters:

depthDistribution - the probability of depth n is depthDistribution[n] for n = 0, 1. . . N - 1

qualityDistribution - the probability of quality q is qualityDistribution[q] for q = 0, 1. . . Q

sampleSize - sample size is the number of random sums of quality scores for each m

logOddsThreshold - is the log_10 of the likelihood ratio required to call a SNP, for example 5 if the variant likelihood must be 10^5 times greater.

withLogging - true to output log messages, false otherwise.

proportionsAboveThresholds

public static java.util.List<java.util.ArrayList<java.lang.Double>> proportionsAboveThresholds(java.util.List<java.util.ArrayList<java.lang.Integer>> lists,
                                                                                               java.util.List<java.lang.Double> thresholds)

hetAltDepthDistribution

public static java.util.List<java.util.ArrayList<java.lang.Double>> hetAltDepthDistribution(int N)

normalizeHistogram

public static double[] normalizeHistogram(htsjdk.samtools.util.Histogram<java.lang.Integer> histogram)