SIGRS
Class SIGRSScoreObject

java.lang.Object
  SIGRS.SIGRSScoreObject

public class SIGRSScoreObject
extends java.lang.Object

SIGRS is a collection of routines used in searching for regions of contrasting composition (CCRs) in sequence files using a partial sum process. Significance of segments is evaluated using Karlin-Altschul statistics and specifically an extension by Karlin-Dembo allowing for nucleotides to have a Markov-dependence (see e.g. Karlin & Altschul (1993) and Karlin & Dembo (1992)

The routines are provided as is and no guarantee regarding stability etc. is given so use at your own risk!

See publication Larsson, P., Hinas, A., Ardell, D.H., Kirsebom, L.A., Virtanen, A. and Söderbom, F. De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring

Questions and comments can be directed to Pontus.Larsson@icm.uu.se

Constructor Summary

SIGRSScoreObject()

Method Summary

void	calculateBackgroundFrequencies(byte[][] backgroundSeqs, LogWriter lw)
static double[][][]	calculateFrequencies(byte[][] seq)
static double[][][]	calculateFrequencies(java.io.File seqFile) Calculates a set of frequencies from a set of input sequences
static double[][][]	calculateFrequencies(int[][] monoCounts, int[][][] diCounts)
void	calculateScores(byte[][] backgroundSeqs, byte[][] targetSeqs, LogWriter lw) Calculates the frequencies, scores and associated parameters for the M0 and M1 model
static double[][]	calculateScores(double[][] background, double[][] target) Calculates score matrix based on target and background frequencies according to s = C*log(tg/bg) and rounded to the closest integer Equivalent to calling calculateScores(background,target,10.,2.)
static double[][]	calculateScores(double[][] background, double[][] target, double C, double base) Calculates score matrix based on target and background frequencies according to s = C*log(tg/bg) and rounded to the closest integer
void	calculateScores(java.io.File backgroundSeqs, java.io.File targetSeqs, LogWriter lw)
void	calculateScores(LogWriter lw)
void	calculateTargetFrequencies(byte[][] targetSeqs, LogWriter lw)
double[][][]	getBackgroundFrequencies() Returns the value of backgroundFrequencies.
double	getH0() Returns the value of H0.
double	getH1() Returns the value of H1.
double	getK0() Returns the value of K0.
double	getK1() Returns the value of K1.
double	getL0() Returns the value of L0.
double	getL1() Returns the value of L1.
double[][]	getM0ScoreMatrix() Returns the value of M0ScoreMatrix.
double[][]	getM1ScoreMatrix() Returns the value of M1ScoreMatrix.
static SIGRSScoreObject	getScoreObject(java.io.File scoreFile, LogWriter lw)
double[][][]	getTargetFrequencies() Returns the value of targetFrequencies.
void	setBackgroundFrequencies(double[][][] backgroundFrequencies) Sets the value of backgroundFrequencies.
void	setH0(double H0) Sets the value of H0.
void	setH1(double H1) Sets the value of H1.
void	setK0(double K0) Sets the value of K0.
void	setK1(double K1) Sets the value of K1.
void	setL0(double L0) Sets the value of L0.
void	setL1(double L1) Sets the value of L1.
void	setM0ScoreMatrix(double[][] M0ScoreMatrix) Sets the value of M0ScoreMatrix.
void	setM1ScoreMatrix(double[][] M1ScoreMatrix) Sets the value of M1ScoreMatrix.
void	setTargetFrequencies(double[][][] targetFrequencies) Sets the value of targetFrequencies.
java.lang.String	toString() Returns a string with the contents of the score object

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SIGRSScoreObject

public SIGRSScoreObject()

Method Detail

getM0ScoreMatrix

public double[][] getM0ScoreMatrix()

Returns the value of M0ScoreMatrix.

setM0ScoreMatrix

public void setM0ScoreMatrix(double[][] M0ScoreMatrix)

Sets the value of M0ScoreMatrix.

Parameters:

M0ScoreMatrix - The value to assign M0ScoreMatrix.

getM1ScoreMatrix

public double[][] getM1ScoreMatrix()

Returns the value of M1ScoreMatrix.

setM1ScoreMatrix

public void setM1ScoreMatrix(double[][] M1ScoreMatrix)

Sets the value of M1ScoreMatrix.

Parameters:

M1ScoreMatrix - The value to assign M1ScoreMatrix.

getBackgroundFrequencies

public double[][][] getBackgroundFrequencies()

Returns the value of backgroundFrequencies.

setBackgroundFrequencies

public void setBackgroundFrequencies(double[][][] backgroundFrequencies)

Sets the value of backgroundFrequencies.

Parameters:

backgroundFrequencies - The value to assign backgroundFrequencies.

getTargetFrequencies

public double[][][] getTargetFrequencies()

Returns the value of targetFrequencies.

setTargetFrequencies

public void setTargetFrequencies(double[][][] targetFrequencies)

Sets the value of targetFrequencies.

Parameters:

targetFrequencies - The value to assign targetFrequencies.

getK0

public double getK0()

Returns the value of K0.

setK0

public void setK0(double K0)

Sets the value of K0.

Parameters:

K0 - The value to assign K0.

getL0

public double getL0()

Returns the value of L0.

setL0

public void setL0(double L0)

Sets the value of L0.

Parameters:

L0 - The value to assign L0.

getH0

public double getH0()

Returns the value of H0.

setH0

public void setH0(double H0)

Sets the value of H0.

Parameters:

H0 - The value to assign H0.

getK1

public double getK1()

Returns the value of K1.

setK1

public void setK1(double K1)

Sets the value of K1.

Parameters:

K1 - The value to assign K1.

getL1

public double getL1()

Returns the value of L1.

setL1

public void setL1(double L1)

Sets the value of L1.

Parameters:

L1 - The value to assign L1.

getH1

public double getH1()

Returns the value of H1.

setH1

public void setH1(double H1)

Sets the value of H1.

Parameters:

H1 - The value to assign H1.

calculateScores

public void calculateScores(byte[][] backgroundSeqs,
                            byte[][] targetSeqs,
                            LogWriter lw)
                     throws java.lang.Exception

Calculates the frequencies, scores and associated parameters for the M0 and M1 model

Parameters:

backgroundSeqs - Array with encoded background sequences

targetSeqs - Array with encoded target sequences

Throws:

java.lang.Exception

calculateScores

public void calculateScores(java.io.File backgroundSeqs,
                            java.io.File targetSeqs,
                            LogWriter lw)
                     throws java.lang.Exception

Throws:

java.lang.Exception

calculateScores

public void calculateScores(LogWriter lw)

calculateBackgroundFrequencies

public void calculateBackgroundFrequencies(byte[][] backgroundSeqs,
                                           LogWriter lw)

calculateTargetFrequencies

public void calculateTargetFrequencies(byte[][] targetSeqs,
                                       LogWriter lw)

calculateFrequencies

public static double[][][] calculateFrequencies(java.io.File seqFile)
                                         throws java.lang.Exception

Calculates a set of frequencies from a set of input sequences

Parameters:

seq - An array of encoded input sequences

Returns:

An array with the different sets of frequencies: [0] -> Mononucleotide frequencies (4x1 array) [1] -> Dinucleotide frequencies (4x4 array) [2] -> Conditional dinucleotide frequencies (4x4 array)

Throws:

java.lang.Exception

calculateFrequencies

public static double[][][] calculateFrequencies(byte[][] seq)

calculateFrequencies

public static double[][][] calculateFrequencies(int[][] monoCounts,
                                                int[][][] diCounts)

calculateScores

public static double[][] calculateScores(double[][] background,
                                         double[][] target)

Calculates score matrix based on target and background frequencies according to s = C*log(tg/bg) and rounded to the closest integer Equivalent to calling calculateScores(background,target,10.,2.)

Parameters:

background - Matrix holding the frequencies of letters in the background

target - Matrix holding the frequencies of letters in the target

Returns:

A score matrix with the same dimensions as the input frequency matrices

calculateScores

public static double[][] calculateScores(double[][] background,
                                         double[][] target,
                                         double C,
                                         double base)

Calculates score matrix based on target and background frequencies according to s = C*log(tg/bg) and rounded to the closest integer

Parameters:

background - Matrix holding the frequencies of letters in the background

target - Matrix holding the frequencies of letters in the target

C - A scaling constant

base - The logarithm base

Returns:

A score matrix with the same dimensions as the input frequency matrices

getScoreObject

public static SIGRSScoreObject getScoreObject(java.io.File scoreFile,
                                              LogWriter lw)
                                       throws java.lang.Exception

Throws:

java.lang.Exception

toString

public java.lang.String toString()

Returns a string with the contents of the score object

Overrides:

toString in class java.lang.Object