halflife
Class HalfLife_New

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

Constructor Summary
HalfLife_New()
           
 
Method Summary
 CorrectionFactors calculateCorrectionFactors(double medianHWZ, double t)
          Calculation of correction factors based on a median
 void calculateHalfLives(int 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 halflife.HalfLife
filterValues, getAlpha, getC_l, getC_u, getData, getHwz, getNewMapping, getRatio, getReplikat, median, ratioOfReplicate, setAlpha, setCorrectionFactors, setHwz, 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 HalfLife 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 HalfLife calculation shall be done
replicate - The replicate that shall be used

calculateHalfLives

public void calculateHalfLives(int 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