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Packages that use Data | |
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halo.data | Provides for the extraction, filtering, handling and saving of expression data. |
halo.examples | Provides easy-to-understand examples for the usage of HALO. |
halo.halflife | Provides for the calculation and handling of half-lives. |
halo.normalization | Provides for the calculation and handling of normalization. |
halo.tools | Provides a set of tools applicable for several uses. |
halo.userinterface.cmdline | Provides for the handling of user input and starting of corresponding calculations. |
halo.userinterface.gui | Provides for the generation and handling of a graphical user interface, as well as the starting of corresponding calculations according to user input. |
halo.userinterface.gui.graphhandler | Provides for generation of plots and histograms. |
halo.userinterface.gui.session | Provides for the handling, saving and loading of sessions and configuration information. |
Uses of Data in halo.data |
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Methods in halo.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> relevantColumns,
java.lang.String call,
int threshold)
Removes values that are defined as 'absent' in the attribute list Commandline option -f present='label1,label2,... |
static Data |
Filter.filterCorrectionBias(Data data,
java.util.HashMap<java.lang.String,java.lang.Double> corr)
Filters the data according to given values for bias correction in such a way that only those probeset ids are kept that have corresponding correction values |
static Data |
Filter.filterPQS(Data data,
Normalization l,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
Filter.filterPQS(Data data,
Normalization l,
double threshold,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
Filter.filterPQS(Data data,
Normalization l,
int replicate,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
Filter.transferAllValues(Data oldData,
Data newData)
Transfers all values that are not directly used in filtering from the old data object to the new data object |
Methods in halo.data with parameters of type Data | |
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static boolean |
Filter.checkForGenes(Data data)
Checks if the data object has the gene name attribute loaded and can be used for PQS filtering |
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> relevantColumns,
java.lang.String call,
int threshold)
Removes values that are defined as 'absent' in the attribute list Commandline option -f present='label1,label2,... |
static Data |
Filter.filterCorrectionBias(Data data,
java.util.HashMap<java.lang.String,java.lang.Double> corr)
Filters the data according to given values for bias correction in such a way that only those probeset ids are kept that have corresponding correction values |
static Data |
Filter.filterPQS(Data data,
Normalization l,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
Filter.filterPQS(Data data,
Normalization l,
double threshold,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
Filter.filterPQS(Data data,
Normalization l,
int replicate,
boolean histogram)
Please note that this method can only be used after normalization! |
static Data |
Filter.transferAllValues(Data oldData,
Data newData)
Transfers all values that are not directly used in filtering from the old data object to the new data object |
Uses of Data in halo.examples |
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Methods in halo.examples that return Data | |
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static Data |
SampleUseCase1.run()
Starts the loading, filtering and printing of data |
Methods in halo.examples with parameters of type Data | |
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static double |
SampleUseCase2.median(Data data,
java.util.ArrayList<HalfLife> medMethods,
double time)
Calculates the median half-life for a set of methods and a given time |
Uses of Data in halo.halflife |
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Methods in halo.halflife that return Data | |
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Data |
HalfLife.getData()
Returns the data object holding the original data |
Methods in halo.halflife with parameters of type Data | |
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void |
HalfLife_New.initialize(Data data)
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void |
HalfLife_NewPre.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_New.initialize(Data data,
int replicate)
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void |
HalfLife_NewPre.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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Uses of Data in halo.normalization |
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Methods in halo.normalization with parameters of type Data | |
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double[] |
Normalization.calculateQualityControl(Data data,
boolean histogram)
Calculates the array containing the quality control values; these are calculated as distance from the normalization line |
Constructors in halo.normalization with parameters of type Data | |
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LinearRegression(Data data)
Constructor for simple linear regression object |
Uses of Data in halo.tools |
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Methods in halo.tools with parameters of type Data | |
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static double |
Tools.calculateMedianForHalfLives(double time,
Data data)
Calculates the average median over two available half-life calculation methods |
Uses of Data in halo.userinterface.cmdline |
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Methods in halo.userinterface.cmdline that return Data | |
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static Data |
CmdNormalization.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 halo.userinterface.cmdline with parameters of type Data | |
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static Normalization |
CmdFilterData.performNormalization(Data data)
Performs normalization on a given Data object with the previously specified method |
static CorrectionFactors |
CmdNormalization.prepareNormalization(Data data)
Contains all the methods for calculation of normalization |
Uses of Data in halo.userinterface.gui |
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Methods in halo.userinterface.gui that return Data | |
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Data |
GuiFilterData.getData()
Returns the complete Data object |
Methods in halo.userinterface.gui with parameters of type Data | |
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void |
GuiNormal.setData(Data data)
Sets the data object for normalization |
void |
GuiHalfLife.setData(Data data)
Sets the data on which the half-life calculation is based |
Uses of Data in halo.userinterface.gui.graphhandler |
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Methods in halo.userinterface.gui.graphhandler with parameters of type Data | |
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static XYGraphConstructor |
GraphHandler.plotNormalization(Normalization norm,
Data data)
Generates the plot for normalization |
Uses of Data in halo.userinterface.gui.session |
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Methods in halo.userinterface.gui.session that return Data | |
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Data |
Session.getData()
Returns the data object |
Methods in halo.userinterface.gui.session with parameters of type Data | |
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void |
Session.setData(Data data)
Sets the data object needed for normalization |
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