Uses of Class
data.Data

Packages that use Data
data   
halflife   
linearregression   
userinterface.cmdline   
userinterface.gui   
 

Uses of Data in data
 

Methods in data that return Data
static Data Filter.filter(Data data, double threshold)
          removes all experiments where at least one of the values is beneath a certain threshold Commandline option -f threshold='value'
static Data Filter.filterAbsent(Data data, java.util.ArrayList<java.lang.String> label)
          Removes values that are defined as 'absent' in the attribute list Commandline option present='label'
static Data Filter.filterPQS(Data data, LinearRegression l)
          Filters data such that from each gene only one entry, the one with the lowest quality control value, is kept Commandline option pqs=min
static Data Filter.filterPQS(Data data, LinearRegression l, double threshold)
          Filters the data in such a way that all remaining entries have a quality control value lower than the given threshold Commandline option pqs='threshold'
 

Methods in data with parameters of type Data
static Data Filter.filter(Data data, double threshold)
          removes all experiments where at least one of the values is beneath a certain threshold Commandline option -f threshold='value'
static Data Filter.filterAbsent(Data data, java.util.ArrayList<java.lang.String> label)
          Removes values that are defined as 'absent' in the attribute list Commandline option present='label'
static Data Filter.filterPQS(Data data, LinearRegression l)
          Filters data such that from each gene only one entry, the one with the lowest quality control value, is kept Commandline option pqs=min
static Data Filter.filterPQS(Data data, LinearRegression l, double threshold)
          Filters the data in such a way that all remaining entries have a quality control value lower than the given threshold Commandline option pqs='threshold'
 

Uses of Data in halflife
 

Methods in halflife that return Data
 Data HalfLife.getData()
          Returns the data object holding the original data
 

Methods in halflife with parameters of type Data
 void HalfLife_New.initialize(Data data)
           
abstract  void HalfLife.initialize(Data data)
          initializes the HalfLife object & extracts the needed values of the Data object
 void HalfLife_Pre.initialize(Data data)
           
 void HalfLife_EU.initialize(Data data)
           
 void HalfLife_New.initialize(Data data, int replicate)
           
abstract  void HalfLife.initialize(Data data, int replicate)
          initializes the HalfLife object for a specific replicate of the data
 void HalfLife_Pre.initialize(Data data, int replicate)
           
 void HalfLife_EU.initialize(Data data, int replicate)
           
 

Uses of Data in linearregression
 

Methods in linearregression with parameters of type Data
 double[] LinearRegression.calculateQualityControl(Data data)
          Calculates the array containing the quality control values; these are calculated as distance from the linear regression line
 

Constructors in linearregression with parameters of type Data
LR_normal(Data data)
          Constructor for simple linear regression object
 

Uses of Data in userinterface.cmdline
 

Methods in userinterface.cmdline that return Data
static Data CmdLinearRegression.getData(java.lang.String[] input)
          Uses the complete options array to split it and forward the necessary information to the interface for data manipulation
static Data CmdFilterData.prepareData(java.lang.String[] input)
          Creates a data object from the information given as options array
 

Methods in userinterface.cmdline with parameters of type Data
static LinearRegression CmdFilterData.performLR(Data data)
          Performs linear regression on a given Data object with the previously specified method
static CorrectionFactors CmdLinearRegression.prepareLR(Data data)
          Contains all the methods for calculation of linear regression
 

Uses of Data in userinterface.gui
 

Methods in userinterface.gui that return Data
 Data GuiFilterData.getData()
          Returns the complete Data object
 Data Session.getData()
          Returns the data object
 

Methods in userinterface.gui with parameters of type Data
 void GuiHalfLife.setData(Data data)
          Sets the data on which the half life calculation is based
 void GuiLinReg.setData(Data data)
          Sets the data object for normalization
 void Session.setData(Data data)
          Sets the data object needed for linear regression