Class TheoreticalSensitivity

Method Details

• 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 List<ArrayList<Double>> proportionsAboveThresholds(List<ArrayList<Integer>> lists, List<Double> thresholds)

• hetAltDepthDistribution

  public static List<ArrayList<Double>> hetAltDepthDistribution(int N)

• normalizeHistogram

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

• sensitivityAtConstantDepth

  public static double sensitivityAtConstantDepth(int depth, htsjdk.samtools.util.Histogram<Integer> qualityHistogram, double logOddsThreshold, int sampleSize, double alleleFraction, long randomSeed)

  Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution at a constant depth.

  Parameters:

  depth - Depth to compute sensitivity at

  qualityHistogram - Phred-scaled quality score histogram

  logOddsThreshold - Log odd threshold necessary for variant to be called

  sampleSize - sampleSize is the total number of simulations to run

  alleleFraction - the allele fraction to evaluate sensitivity at

  randomSeed - random number seed to use for random number generator

  Returns:

  Theoretical sensitivity for the given arguments at a constant depth.

• theoreticalSensitivity

  public static double theoreticalSensitivity(htsjdk.samtools.util.Histogram<Integer> depthHistogram, htsjdk.samtools.util.Histogram<Integer> qualityHistogram, int sampleSize, double logOddsThreshold, double alleleFraction)

  Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution and depth distribution.

  Parameters:

  depthHistogram - Depth histogram to compute theoretical sensitivity over

  qualityHistogram - Phred-scaled quality score histogram

  sampleSize - the total number of simulations to run

  logOddsThreshold - Log odds threshold necessary for variant to be called

  alleleFraction - the allele fraction to evaluate sensitivity at

  Returns:

  Theoretical sensitivity for the given arguments over a particular depth distribution.

• calculateSensitivities

  public static List<TheoreticalSensitivityMetrics> calculateSensitivities(int simulationSize, htsjdk.samtools.util.Histogram<Integer> depthHistogram, htsjdk.samtools.util.Histogram<Integer> baseQHistogram, List<Double> alleleFractions)

  This is a utility function to calculate the metrics specific to running theoretical sensitivity over several different allele fractions.

  Parameters:

  simulationSize - Number of simulations to run at each depth.

  depthHistogram - Histogram of depth distribution.

  baseQHistogram - Histogram of Phred-scaled quality scores.

  alleleFractions - List of allele fractions to measure theoretical sensitivity over.