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calcHL()
- Method in class halo.userinterface.gui.
GuiHalfLife
Use set variables and create HalfLife objects for every method, calculate half-lives
calcHLonMedian(List<CorrectionFactors>)
- Method in class halo.userinterface.gui.
GuiHalfLife
Calculates the half-life values based on a list of correction factors which correspond to the list of half-lives
calcNormalization()
- Method in class halo.userinterface.gui.
GuiNormal
Creates Normalization object and performs normalization
calculateAverageFirst(double[][], double[][], HashMap<String, Double>)
- Method in class halo.data.
Data
Calculates the average values from all replicates for the linear regression through calculating the ratio of the averages (AVERAGEFIRST method).
calculateCorrectionFactors(double, double)
- Method in class halo.halflife.
HalfLife
Calculation of correction factors based on a median
calculateCorrectionFactors(double, double)
- Method in class halo.halflife.
HalfLife_New
calculateCorrectionFactors(double, double)
- Method in class halo.halflife.
HalfLife_NewPre
calculateCorrectionFactors(double, double)
- Method in class halo.halflife.
HalfLife_Pre
calculateCorrectionFactors()
- Method in class halo.normalization.
LinearRegression
calculateCorrectionFactors()
- Method in class halo.normalization.
Normalization
calculates correction factors via normalization methods
calculateCorrectionFactors(int)
- Method in class halo.normalization.
Normalization
Calculates the correction factors for a certain replicate
calculateCorrelationCoefficient()
- Method in class halo.data.biascorrection.
CorrelationCoefficient
Abstract method for the calculation of the correlation coefficient for the data
calculateCorrelationCoefficient()
- Method in class halo.data.biascorrection.
RCorrelationCoefficient
Start the calculation of the correlation coefficient
calculateHalfLives(double)
- Method in class halo.halflife.
HalfLife
Calculation of half-lives
calculateHalfLives(double)
- Method in class halo.halflife.
HalfLife_New
calculateHalfLives(double)
- Method in class halo.halflife.
HalfLife_NewPre
calculateHalfLives(double)
- Method in class halo.halflife.
HalfLife_Pre
calculateLoessRegression()
- Method in class halo.data.biascorrection.
LoessRegression
Abstract method for the calculation of the fitted values for correction of bias
calculateLoessRegression()
- Method in class halo.data.biascorrection.
RLoessRegression
Starts the calculation of the fitted values with R
calculateMappingForAttributes(String[][], String[])
- Method in class halo.data.
Data
Transcribes the attributes into a mapping id -> attribute.
calculateMedian()
- Method in class halo.userinterface.gui.
GuiHalfLife
Calculate the median for a set of half-lives
calculateMedianForHalfLives(double, Data)
- Static method in class halo.tools.
Tools
Calculates the average median over two available half-life calculation methods
calculateNewMapping()
- Method in class halo.data.
Data
Calculates the Mapping corresponding to the ratio.
calculateQualityControl(Data, boolean)
- Method in class halo.normalization.
Normalization
Calculates the array containing the quality control values; these are calculated as distance from the normalization line
calculateRatio(double[][], double[][], HashMap<String, Double>, int)
- Method in class halo.data.
Data
Calculates filtered Ratio of a set of RNA values (e.g. newly transcribed RNA) to a second set of values (e.g. total RNA) based on the specified method to calculate the average of multiple replicates.
calculateRatio(double[][], double[][], HashMap<String, Double>)
- Method in class halo.data.
Data
Calculates the ratios for an average over a set of replicates.
calculateRatioFirst(double[][])
- Method in class halo.data.
Data
calculates the average values from all replicates for the linear regression.
changeMap(T, U)
- Method in class halo.data.
Mapping
Change the attribute of a specific spotID
checkForGenes(Data)
- Static method in class halo.data.
Filter
Checks if the data object has the gene name attribute loaded and can be used for PQS filtering
clearHL()
- Method in class halo.userinterface.gui.
GuiHalfLife
Resets everything that has been used for half-life calculation of previous half-life list
close()
- Method in class halo.userinterface.gui.guitools.
LabelChooserDialog
Hides the dialog window
CmdFilterData
- Class in
halo.userinterface.cmdline
Serves as interface between Data manipulation tools and command line input
CmdFilterData()
- Constructor for class halo.userinterface.cmdline.
CmdFilterData
CmdHalfLife
- Class in
halo.userinterface.cmdline
Serves as interface between command line input and calculation of half-lives
CmdHalfLife()
- Constructor for class halo.userinterface.cmdline.
CmdHalfLife
CmdNormalization
- Class in
halo.userinterface.cmdline
Serves as interface between command line input and tools for calculation of linear regression
CmdNormalization()
- Constructor for class halo.userinterface.cmdline.
CmdNormalization
CommandLine
- Class in
halo.userinterface.cmdline
Class which forwards information from command line input to further classes which serve as interface between command line and tools for calculation
CommandLine()
- Constructor for class halo.userinterface.cmdline.
CommandLine
compareTo(Object)
- Method in class halo.tools.
Tuple
Config
- Class in
halo.userinterface.gui.session
Provides a set of final parameters describing paths and file names and saves user decisions for the display of certain dialogs
Config()
- Constructor for class halo.userinterface.gui.session.
Config
CONFIGDIR
- Static variable in class halo.userinterface.gui.session.
Config
CONFIGFILE
- Static variable in class halo.userinterface.gui.session.
Config
CONFIGPATH
- Static variable in class halo.userinterface.gui.session.
Config
containsAttribute(U)
- Method in class halo.data.
Mapping
Returns true if the given attribute exists in the Mapping
containsSpot(T)
- Method in class halo.data.
Mapping
Returns true if the given key exists in the Mapping
copyMap()
- Method in class halo.data.
Data
Copies the content of the Mapping object.
CorrectionFactors
- Class in
halo.normalization
Class for managing the correction factors needed for half-life calculation
CorrectionFactors()
- Constructor for class halo.normalization.
CorrectionFactors
Constructor setting the factors to the default value UNDEF = -1
CorrectionFactors(double, double)
- Constructor for class halo.normalization.
CorrectionFactors
Constructor setting only the factors c_l and c_u
CorrectionFactors(double)
- Constructor for class halo.normalization.
CorrectionFactors
Constructor setting only the factor c_lu
CorrectionFactors(double, double, double)
- Constructor for class halo.normalization.
CorrectionFactors
Constructor setting all three correction factors
CorrelationCoefficient
- Class in
halo.data.biascorrection
Abstract class for the calculation of the correlation coefficient of a data set
CorrelationCoefficient()
- Constructor for class halo.data.biascorrection.
CorrelationCoefficient
CORRELATIONCOEFFICIENT
- Static variable in class halo.userinterface.gui.session.
Config
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