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java.lang.Objecthalo.halflife.HalfLife
public abstract class HalfLife
Calculation of half-lives and median-based Correction Factors
Field Summary | |
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static java.lang.String |
NEWLY
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static java.lang.String |
NEWPRE
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static java.lang.String |
PRE
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Constructor Summary | |
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HalfLife()
Constructs a HalfLife object with default Alpha |
Method Summary | |
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abstract CorrectionFactors |
calculateCorrectionFactors(double medianHWZ,
double t)
Calculation of correction factors based on a median |
abstract void |
calculateHalfLives(double t)
Calculation of half-lives |
Alpha |
getAlpha()
Returns the alpha object defining the calculation method of alpha |
double |
getC_l()
Returns the correction factor c_l |
double |
getC_u()
Returns the correction factor c_u |
Data |
getData()
Returns the data object holding the original data |
double[] |
getHwz()
Returns the half-life values |
double |
getMax()
Returns the highest present half-life value |
static double |
getMaximumHalfLife()
Returns the set maximum half-life |
static double |
getMinimumHalfLife()
Returns the set minimum half-life |
java.lang.String |
getName()
Returns the name of this method |
Mapping<java.lang.String,java.lang.Integer> |
getNewMapping()
Returns the mapping corresponding to ratios/half-lives |
double[] |
getRatio()
Returns the ratio values |
int |
getReplicate()
Returns the number of the used replicate |
abstract void |
initialize(Data data)
initializes the HalfLife object & extracts the needed values of the Data object |
abstract void |
initialize(Data data,
int replicate)
initializes the HalfLife object for a specific replicate of the data |
static double |
median(double[] inp)
Calculation of the median of a single dimensional array |
void |
printHalfLivesWithAttributes(java.lang.String file,
java.util.ArrayList<java.lang.String> labels)
Prints half-life values together with a given list of attributes into an output file |
double[] |
ratioOfReplicate(double[][] rna,
double[][] total)
Calculates the ratio of a specific replicate |
void |
setAlpha(Alpha alpha)
Sets the Alpha object defining the method for calculation of alpha(t) |
abstract void |
setCorrectionFactor(CorrectionFactors corr)
Sets the set of correction factors |
void |
setCorrectionFactors(double c_u,
double c_l)
Sets the correction factors c_u and c_l |
void |
setHwz(double[] hwz)
Sets the half-life values |
static void |
setMaximumHalfLife(double maximumHalfLife)
Sets the maximum half-life value to be used |
static void |
setMinimumHalfLife(double minimumHalfLife)
Sets the minimal half-life value to be used |
void |
setNewMap(Mapping<java.lang.String,java.lang.Integer> newMap)
Sets the mapping corresponding to the ratio values |
void |
writeToFileHalfLives(java.lang.String output)
Writes the half-life values contained in the object together with corresponding spotIds into a file |
void |
writeToFileRatios(java.lang.String output)
Writes Ratio array into a file with two columns: column 1: spotID, column 2: corresponding ratio |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String NEWLY
public static final java.lang.String PRE
public static final java.lang.String NEWPRE
Constructor Detail |
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public HalfLife()
Method Detail |
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public abstract void initialize(Data data)
data
- The data object for which the half-life calculation shall be donepublic abstract void initialize(Data data, int replicate)
data
- The data object for which the half-life calculation shall be donereplicate
- The replicate that shall be usedpublic abstract void calculateHalfLives(double t)
t
- Timepublic abstract CorrectionFactors calculateCorrectionFactors(double medianHWZ, double t)
medianHWZ
- median mRNA half-lifet
- Time
public static double median(double[] inp)
inp
- The array for which the median shall be calculated
public double[] ratioOfReplicate(double[][] rna, double[][] total)
rna
- Set of RNA values serving as numeratortotal
- Set of RNA values serving as denominator
public void writeToFileHalfLives(java.lang.String output)
output
- Name of output filepublic void writeToFileRatios(java.lang.String output)
output
- The name of the file for the outputpublic void printHalfLivesWithAttributes(java.lang.String file, java.util.ArrayList<java.lang.String> labels)
file
- The name of the output filelabels
- The labels of attributespublic void setNewMap(Mapping<java.lang.String,java.lang.Integer> newMap)
newMap
- The mapping corresponding to the ratiospublic void setAlpha(Alpha alpha)
alpha
- The alpha objectpublic abstract void setCorrectionFactor(CorrectionFactors corr)
corr
- The correction factorspublic void setHwz(double[] hwz)
hwz
- The half-life valuespublic void setCorrectionFactors(double c_u, double c_l)
c_u
- The correction factor c_uc_l
- The correction factor c_lpublic static void setMaximumHalfLife(double maximumHalfLife)
maximumHalfLife
- Maximum half-lifepublic static void setMinimumHalfLife(double minimumHalfLife)
minimumHalfLife
- Minimum half-lifepublic Alpha getAlpha()
public double getMax()
public java.lang.String getName()
public double getC_l()
public double getC_u()
public Mapping<java.lang.String,java.lang.Integer> getNewMapping()
public Data getData()
public double[] getHwz()
public double[] getRatio()
public int getReplicate()
public static double getMinimumHalfLife()
public static double getMaximumHalfLife()
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