Package ubic.basecode.math.linearmodels

Class DesignMatrix

java.lang.Object

ubic.basecode.math.linearmodels.DesignMatrix

public class DesignMatrix
extends Object

Represents the A matrix in regression problems posed as Ax=b. The starting point is a matrix of sample information, where the rows are sample names and the columns are the names of factors or covariates. Intercept and interaction terms can be added.

Baseline levels are initially determined by the order in which factor levels appear. You can re-level using the setBaseline method.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
DesignMatrix(Object[] factor, int start, String factorName)
DesignMatrix(ObjectMatrix<String,String,?> sampleInfo, boolean intercept)
DesignMatrix(ObjectMatrix<String,String,? extends Object> sampleInfo)
DesignMatrix(ObjectMatrix<String,String,Object> design, boolean intercept, boolean strict)
DesignMatrix(StringMatrix<String,String> sampleInfo)

Method Summary

Modifier and Type	Method	Description
void	add(ObjectMatrix<String,String,Object> sampleInfo)	Append additional factors/covariates to this
void	addInteraction()	Add interaction term; only works if there exactly two factors so this can figure out which interaction to add.
void	addInteraction(String... interactionTerms)	This will not add the interaction unless all of the terms are already part of the design, and interactions that obviously can't be estimated will be dropped if possible, but otherwise this is fairly brain dead.
List<Integer>	getAssign()
String	getBaseline(String factorName)
cern.colt.matrix.DoubleMatrix2D	getDoubleMatrix()
Collection<String[]>	getInteractionTerms()
Map<String,List<String>>	getLevelsForFactors()
DoubleMatrix<String,String>	getMatrix()
List<String>	getTerms()
Map<String,List<Object>>	getValuesForFactors()
boolean	hasIntercept()
boolean	isHasIntercept()
cern.colt.matrix.DoubleMatrix2D	makeContrasts()	In limma, the contrasts are built by referring to the coefficients by name, which isn't what we want.
protected void	rebuild()	Refresh the design matrix, for example after releveling.
void	setBaseline(String factorName, String baselineFactorValue)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

DesignMatrix

public DesignMatrix(Object[] factor,
                    int start,
                    String factorName)

Parameters:

factor - in form of Doubles or Strings. Any other types will yield errors.

start -

DesignMatrix

public DesignMatrix(ObjectMatrix<String,String,? extends Object> sampleInfo)

Parameters:

sampleInfo - in form of Doubles or Strings. Any other types will yield errors.

DesignMatrix

public DesignMatrix(ObjectMatrix<String,String,?> sampleInfo,
                    boolean intercept)

Parameters:

sampleInfo - in form of Doubles or Strings. Any other types will yield errors.

intercept -

DesignMatrix

public DesignMatrix(StringMatrix<String,String> sampleInfo)

DesignMatrix

public DesignMatrix(ObjectMatrix<String,String,Object> design,
                    boolean intercept,
                    boolean strict)

Parameters:

design -

intercept - whether to include an intercept in the model

strict - whether to remove columns from the design matrix that are unlikely to be useable. By default this is "true" for other constructors.

Method Detail

getInteractionTerms

public Collection<String[]> getInteractionTerms()

Returns:

a collection of String arrays. If empty, there are no interactions. Each array represents an interaction in the model. The elements of the array are the terms included in the interaction, as Strings provided when calling addInteraction.

makeContrasts

public cern.colt.matrix.DoubleMatrix2D makeContrasts()

In limma, the contrasts are built by referring to the coefficients by name, which isn't what we want.

Returns:

add

public void add(ObjectMatrix<String,String,Object> sampleInfo)

Append additional factors/covariates to this

Parameters:

sampleInfo -

addInteraction

public void addInteraction()

Add interaction term; only works if there exactly two factors so this can figure out which interaction to add. For more control use the other method.

addInteraction

public void addInteraction(String... interactionTerms)

This will not add the interaction unless all of the terms are already part of the design, and interactions that obviously can't be estimated will be dropped if possible, but otherwise this is fairly brain dead.

Parameters:

interactionTerms -

getAssign

public List<Integer> getAssign()

Returns:

getBaseline

public String getBaseline(String factorName)

getDoubleMatrix

public cern.colt.matrix.DoubleMatrix2D getDoubleMatrix()

getLevelsForFactors

public Map<String,List<String>> getLevelsForFactors()

getMatrix

public DoubleMatrix<String,String> getMatrix()

getTerms

public List<String> getTerms()

getValuesForFactors

public Map<String,List<Object>> getValuesForFactors()

hasIntercept

public boolean hasIntercept()

isHasIntercept

public boolean isHasIntercept()

setBaseline

public void setBaseline(String factorName,
                        String baselineFactorValue)

Parameters:

factorName -

baselineFactorValue -

toString

public String toString()

Overrides:

toString in class Object

rebuild

protected void rebuild()

Refresh the design matrix, for example after releveling.