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Packages that use Data | |
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data | |
halflife | |
linearregression | |
userinterface.cmdline | |
userinterface.gui |
Uses of Data in data |
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Methods in data that return Data | |
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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 | |
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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 |
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Methods in halflife that return Data | |
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Data |
HalfLife.getData()
Returns the data object holding the original data |
Methods in halflife with parameters of type Data | |
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void |
HalfLife_New.initialize(Data data)
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abstract void |
HalfLife.initialize(Data data)
initializes the HalfLife object & extracts the needed values of the Data object |
void |
HalfLife_Pre.initialize(Data data)
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void |
HalfLife_EU.initialize(Data data)
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void |
HalfLife_New.initialize(Data data,
int replicate)
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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)
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void |
HalfLife_EU.initialize(Data data,
int replicate)
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Uses of Data in linearregression |
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Methods in linearregression with parameters of type Data | |
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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 | |
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LR_normal(Data data)
Constructor for simple linear regression object |
Uses of Data in userinterface.cmdline |
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Methods in userinterface.cmdline that return Data | |
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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 | |
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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 |
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Methods in userinterface.gui that return Data | |
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Data |
GuiFilterData.getData()
Returns the complete Data object |
Data |
Session.getData()
Returns the data object |
Methods in userinterface.gui with parameters of type Data | |
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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 |
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