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java.lang.Objectorg.gersteinlab.regulation.TrajectoryProfile
public class TrajectoryProfile
A class for storing the trajectory profile of all genes read from a file.
Change History: 1.0 - Initial version
Field Summary | |
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protected double[][][] |
dydt
|
protected int |
expCount
|
protected int |
geneCount
|
protected java.lang.String[] |
geneNames
|
protected int |
pointCount
|
protected int |
polyDeg
|
protected double[][][] |
profile
|
protected double[][][] |
profile2
|
protected double[] |
t
|
protected double[] |
xs
|
protected double[][][] |
y
|
Constructor Summary | |
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protected |
TrajectoryProfile(java.io.Reader r,
int polyDegIn)
Constructor. |
Method Summary | |
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double |
getResidual(int j,
int[][] ks,
java.lang.Class<? extends RateModel> modelClass,
double[] a0)
Get the residual when using some genes k to predict the expression of a gene j based on the best fit of a rate model starting from an initial set of parameter values. |
double |
getResidual(int j,
int[][] ks,
java.lang.Class<? extends RateModel> modelClass,
double[] aStar,
int iter,
double[] mins,
double[] maxs)
Get the residual when using some genes k to predict the expression of a gene j based on the best fit of a rate model starting from random parameter values. |
static TrajectoryProfile |
readProfile(java.io.Reader r,
int polyDegIn)
Read and return the profile in a file. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected int geneCount
protected java.lang.String[] geneNames
protected int expCount
protected int pointCount
protected double[][][] profile
protected int polyDeg
protected double[][][] profile2
protected double[] xs
protected double[] t
protected double[][][] y
protected double[][][] dydt
Constructor Detail |
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protected TrajectoryProfile(java.io.Reader r, int polyDegIn) throws java.io.IOException
r
- The reader of the filepolyDegIn
- Degree of polynomial for smoothing the trajectories
java.io.IOException
Method Detail |
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public static TrajectoryProfile readProfile(java.io.Reader r, int polyDegIn) throws java.io.IOException
r
- The reader of the filepolyDegIn
- Degree of polynomial for smoothing the trajectories
java.io.IOException
public double getResidual(int j, int[][] ks, java.lang.Class<? extends RateModel> modelClass, double[] aStar, int iter, double[] mins, double[] maxs) throws java.lang.InstantiationException, java.lang.IllegalAccessException, java.lang.IllegalArgumentException, java.lang.reflect.InvocationTargetException, java.lang.NoSuchMethodException
j
- The gene whose expression is to be predictedks
- The genes to be used to make the predictions
First dimension: predictor set
Second dimension: predictorsmodelClass
- The class of the rate modelaStar
- For specifying the number of parameters and
storing the final parameter valuesiter
- The number of random initial parameter sets to trymins
- Minimum of parameter valuesmaxs
- Maximum of parameter values
java.lang.InstantiationException
java.lang.IllegalAccessException
java.lang.IllegalArgumentException
java.lang.reflect.InvocationTargetException
java.lang.NoSuchMethodException
public double getResidual(int j, int[][] ks, java.lang.Class<? extends RateModel> modelClass, double[] a0) throws java.lang.InstantiationException, java.lang.IllegalAccessException, java.lang.IllegalArgumentException, java.lang.reflect.InvocationTargetException, java.lang.NoSuchMethodException
j
- The gene whose expression is to be predictedks
- The genes to be used to make the predictions
First dimension: predictor set
Second dimension: predictorsmodelClass
- The class of the rate modela0
- The initial parameter values. The final values will be
stored back to this array.
java.lang.InstantiationException
java.lang.IllegalAccessException
java.lang.IllegalArgumentException
java.lang.reflect.InvocationTargetException
java.lang.NoSuchMethodException
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