Class GeneGeneDist

java.lang.Object
  |
  +--GeneGeneDist

class GeneGeneDist

extends java.lang.Object

Field Summary

private static Config	cfg link to global Config instance
private static float[]	cv1Tmp temporary v1 vector[0:nEP-1] for computations
private static float[]	cv1TmpEP temporary EP v1 vector[0:nEP-1] for computations
private static float[]	cv2Tmp temporary v2 vector[0:nEP-1] for computations
private static float[]	cv2TmpEP temporary EP v2 vector[0:nEP-1] for computations
(package private) GeneList	dataCL Gene list to generate geneEPvector
private static FileIO	fio link to global FileIO instance
(package private) float[][]	geneEPvector normalized quantitation vector for all genes [0:nClist-1][0:nEP-1] also [0:nObj-1][0:nEP-1]
private SampleSets	hps link to global SampleSets instance
private static MAExplorer	mae link to global MAExplorer instance
(package private) int	nEP size of EP vector
(package private) int	nMlist # of genes

Constructor Summary

(package private)

GeneGeneDist(MAExplorer mae) GeneGeneDist() - constructor

Method Summary

private static int	addr1D(int x, int y) addr1D() - lookup lower-diagonal addr1D(x,y) using [y' + x'*(x'+1)/2] address
(package private) void	calcGeneGeneDists(float[] ccDist1D, int nClist, int nEP) calcGeneGeneDists() - compute the gene-gene Euclidean distances for all dataCL genes in the lower diagonal matrix.
(package private) float[][]	calcNormGeneVectors(GeneList dataCL, int nClist) calcNormGeneVectors() - compute HP-E intensity vector for dataCL.mList[].
(package private) void	cleanup() cleanup() - cleanup global static allocated variables in this class.
(package private) float	clusterDistance(Gene geneI, Gene geneJ) clusterDistance() - compute genes(I,J) cluster distance for HP-E samples.
(package private) static int	findGeneWithLeastSumDistances(float[] ccDist1D, int nClist) findGeneWithLeastSumDistances() - find gene with minimum cluster distance toall other genes.
(package private) float	geneGeneDist(float[] geneEPvector1, float[] geneEPvector2, int nEP) geneGeneDist() - compute the gene-gene distance between two gene vectors.
private void	makeTmpVectors(int n) makeTmpVectors() - create temp vectors if needed.

Methods inherited from class java.lang.Object

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

Field Detail

mae

private static MAExplorer mae

link to global MAExplorer instance

fio

private static FileIO fio

link to global FileIO instance

cfg

private static Config cfg

link to global Config instance

hps

private SampleSets hps

link to global SampleSets instance

dataCL

GeneList dataCL

Gene list to generate geneEPvector

nMlist

int nMlist

# of genes

nEP

int nEP

size of EP vector

cv1Tmp

private static float[] cv1Tmp

temporary v1 vector[0:nEP-1] for computations

cv2Tmp

private static float[] cv2Tmp

temporary v2 vector[0:nEP-1] for computations

cv1TmpEP

private static float[] cv1TmpEP

temporary EP v1 vector[0:nEP-1] for computations

cv2TmpEP

private static float[] cv2TmpEP

temporary EP v2 vector[0:nEP-1] for computations

geneEPvector

float[][] geneEPvector

normalized quantitation vector for all genes [0:nClist-1][0:nEP-1] also [0:nObj-1][0:nEP-1]

Constructor Detail

GeneGeneDist

GeneGeneDist(MAExplorer mae)

GeneGeneDist() - constructor

Parameters:

mae - is instance of MAExplorer

Method Detail

makeTmpVectors

private void makeTmpVectors(int n)

makeTmpVectors() - create temp vectors if needed.

calcNormGeneVectors

float[][] calcNormGeneVectors(GeneList dataCL,
                              int nClist)

calcNormGeneVectors() - compute HP-E intensity vector for dataCL.mList[]. Normalize by the first entry of each vector.

Parameters:

dataCL - is the gene list to use

nClist - is the # of genes in the gene list

Returns:

a dynamic array[nClist][nEP].

See Also:

MaHybridSample.getDataByGID(int, boolean, int), MathMAE.calcPearsonCorrCoef(float[], float[], int, boolean), MathMAE.euclidDist(float[], float[], int, boolean), makeTmpVectors(int)

geneGeneDist

float geneGeneDist(float[] geneEPvector1,
                   float[] geneEPvector2,
                   int nEP)

geneGeneDist() - compute the gene-gene distance between two gene vectors. Note: can either compute the difference with the magnitude either scaled or unscaled Unscaled the data from the current global normalization method. Unscaled is just the distance of the two gebne vectors. Normalized sets the max of each vector to 1.0 before doing the difference. This means we could have two different EPs with the same shape but different magnitudes. They would be picked up by the second, but not the first method.

Parameters:

geneEPvector1 - is the gene vector for gene 1

geneEPvector2 - is the gene vector for gene 2

nEP - is the number of samples if used w/o HP-E list

Returns:

computed cluster distance.

clusterDistance

float clusterDistance(Gene geneI,
                      Gene geneJ)

clusterDistance() - compute genes(I,J) cluster distance for HP-E samples.

Parameters:

geneI - is first gene

geneJ - is 2nd gene

Returns:

computed cluster distance based on global switches.

See Also:

MaHybridSample.getDataByGID(int, boolean, int), geneGeneDist(float[], float[], int), makeTmpVectors(int)

addr1D

private static final int addr1D(int x,
                                int y)

addr1D() - lookup lower-diagonal addr1D(x,y) using [y' + x'*(x'+1)/2] address

 where:
    x' = (x>y) ? x : y,
    y' = (x>y) ? y : x.

Parameters:

x - coordinate

y - coordinate

Returns:

the computed 1D address for the 2D (x,y) address.

calcGeneGeneDists

void calcGeneGeneDists(float[] ccDist1D,
                       int nClist,
                       int nEP)

calcGeneGeneDists() - compute the gene-gene Euclidean distances for all dataCL genes in the lower diagonal matrix. Only need to do the assymetric case Cij (j>i) since Cij == Cji.

Parameters:

ccDist1D - is 1D list emulating 2D list of Cijk distances for sample k

nClist - number of genes to compute

nEP - is the number of samples in ccDist1D list

See Also:

Util.showMsg2(java.lang.String), addr1D(int, int), geneGeneDist(float[], float[], int)

findGeneWithLeastSumDistances

static int findGeneWithLeastSumDistances(float[] ccDist1D,
                                         int nClist)

findGeneWithLeastSumDistances() - find gene with minimum cluster distance toall other genes.

Parameters:

ccDist1D - is 1D list emulating 2D list of Cijk distances for sample k

nClist - number of genes to compute

Returns:

the index or -1 if not found.

See Also:

addr1D(int, int)

cleanup

void cleanup()

cleanup() - cleanup global static allocated variables in this class. If statics are added later to this class, then set them to null here.