net.sf.snver.pileup.util.math
Class BinomBinom

java.lang.Object
  net.sf.snver.pileup.util.math.BinomBinom

public class BinomBinom
extends java.lang.Object

Constructor Summary

BinomBinom()

Method Summary

static double	dbinombinom(int x, int n, int m, double e, double theta0)
static double	pool_binom(int x, int n, int m, double e, double theta0)

Methods inherited from class java.lang.Object

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

Constructor Detail

BinomBinom

public BinomBinom()

Method Detail

dbinombinom

public static double dbinombinom(int x,
                                 int n,
                                 int m,
                                 double e,
                                 double theta0)

Parameters:

x - observed the most freq non-ref allele counts

n - individuals

m - short reads cover this locus

e - sequencing error rate

theta0 - minor allele frequency threshold

Returns:

probality of X

pool_binom

public static double pool_binom(int x,
                                int n,
                                int m,
                                double e,
                                double theta0)

Parameters:

x - observed the most freq non-ref allele counts

n - individuals

m - short reads cover this locus

e - sequencing error rate

theta0 - minor allele frequency threshold

Returns:

p-value of whether this locus is a (rare) variant (theta>theta0)