halo.halflife
Class HalfLife_New

java.lang.Object
  extended by halo.halflife.HalfLife
      extended by halo.halflife.HalfLife_New

public class HalfLife_New
extends HalfLife

Implementation of HalfLife providing methods for the usual calculation of half-life values for newly transcribed RNA, based on the ratio of newly transcribed to total RNA

Author:
Stefanie Kaufmann

Field Summary
 
Fields inherited from class halo.halflife.HalfLife
NEWLY, NEWPRE, PRE
 
Constructor Summary
HalfLife_New()
           
 
Method Summary
 CorrectionFactors calculateCorrectionFactors(double medianHWZ, double t)
          Calculation of correction factors based on a median
 void calculateHalfLives(double t)
          Calculation of half-lives
 void initialize(Data data)
          initializes the HalfLife object & extracts the needed values of the Data object
 void initialize(Data data, int replicate)
          initializes the HalfLife object for a specific replicate of the data
 void setCorrectionFactor(CorrectionFactors corr)
          Sets the set of correction factors
 
Methods inherited from class halo.halflife.HalfLife
getAlpha, getC_l, getC_u, getData, getHwz, getMax, getMaximumHalfLife, getMinimumHalfLife, getName, getNewMapping, getRatio, getReplicate, median, printHalfLivesWithAttributes, ratioOfReplicate, setAlpha, setCorrectionFactors, setHwz, setMaximumHalfLife, setMinimumHalfLife, setNewMap, writeToFileHalfLives, writeToFileRatios
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

HalfLife_New

public HalfLife_New()
Method Detail

initialize

public void initialize(Data data)
Description copied from class: HalfLife
initializes the HalfLife object & extracts the needed values of the Data object

Specified by:
initialize in class HalfLife
Parameters:
data - The data object for which the half-life calculation shall be done

initialize

public void initialize(Data data,
                       int replicate)
Description copied from class: HalfLife
initializes the HalfLife object for a specific replicate of the data

Specified by:
initialize in class HalfLife
Parameters:
data - The data object for which the half-life calculation shall be done
replicate - The replicate that shall be used

calculateHalfLives

public void calculateHalfLives(double t)
Description copied from class: HalfLife
Calculation of half-lives

Specified by:
calculateHalfLives in class HalfLife
Parameters:
t - Time

calculateCorrectionFactors

public CorrectionFactors calculateCorrectionFactors(double medianHWZ,
                                                    double t)
Description copied from class: HalfLife
Calculation of correction factors based on a median

Specified by:
calculateCorrectionFactors in class HalfLife
Parameters:
medianHWZ - median mRNA half-life
t - Time
Returns:
CorrectionFactors c_u and c_l

setCorrectionFactor

public void setCorrectionFactor(CorrectionFactors corr)
Description copied from class: HalfLife
Sets the set of correction factors

Specified by:
setCorrectionFactor in class HalfLife
Parameters:
corr - The correction factors