halo.data
Class Data

java.lang.Object
  extended by halo.data.Data

public class Data
extends java.lang.Object

Reading and containing RNA values from an input file and providing methods for the calculation of RNA ratios as well as methods to save the filtered values to a file.

Author:
Stefanie Kaufmann

Field Summary
static int AVERAGEFIRST
           
static java.lang.String GENEDEFAULT
           
static java.lang.String LOGEN
           
static java.lang.String LOGEU
           
static java.lang.String LOGUN
           
static int RATIOFIRST
           
static int REPLICATE
           
 
Constructor Summary
Data()
          Constructs an empty Data-Object, so that parameters for data loading can be set before starting.
Data(double[][] totalRNA, double[][] newRNA, double[][] preRNA, java.lang.String[] totalDescr, java.lang.String[] newDescr, java.lang.String[] preDescr, Mapping<java.lang.String,java.lang.Integer> map)
          Constructs a Data-Object based on already existing data.
Data(java.lang.String file, java.util.List<java.lang.String> columnsTotal, java.util.List<java.lang.String> columnsNew, java.util.List<java.lang.String> columnsPre, boolean log)
          Constructs a Data-Object based on an Input-File and the list of columns to be read with no additional attributes.
Data(java.lang.String file, java.util.List<java.lang.String> columnsTotal, java.util.List<java.lang.String> columnsNew, java.util.List<java.lang.String> columnsPre, java.util.List<java.lang.String> attr, boolean log)
          Constructs a Data-Object based on an Input-File and the list of columns to be read, defines columns containing attributes.
 
Method Summary
 void addAttributes(java.lang.String inputfile)
          Reads in every attribute from a given file.
 void addAttributes(java.lang.String inputfile, java.util.ArrayList<java.lang.String> columnLabels)
          Reads in regular attributes from a file.
 void addAttributes(java.lang.String inputfile, java.util.ArrayList<java.lang.String> columnLabels, boolean turnReverseMapOff)
          Reads in a file containing several columns, of which one contains the spotID, the others contain attributes.
 void addPresenceCalls(java.lang.String inputfile, java.util.ArrayList<java.lang.String> columnLabels)
          Reads in attributes from a file.
 double[] calculateAverageFirst(double[][] rna, double[][] total, java.util.HashMap<java.lang.String,java.lang.Double> corr)
          Calculates the average values from all replicates for the linear regression through calculating the ratio of the averages (AVERAGEFIRST method).
 void calculateMappingForAttributes(java.lang.String[][] allAttributes, java.lang.String[] ids)
          Transcribes the attributes into a mapping id -> attribute.
 Mapping<java.lang.String,java.lang.Integer> calculateNewMapping()
          Calculates the Mapping corresponding to the ratio.
 double[] calculateRatio(double[][] rna, double[][] total, java.util.HashMap<java.lang.String,java.lang.Double> corr)
          Calculates the ratios for an average over a set of replicates.
 double[] calculateRatio(double[][] rna, double[][] total, java.util.HashMap<java.lang.String,java.lang.Double> corr, int replicate)
          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.
 double[] calculateRatioFirst(double[][] allRatio)
          calculates the average values from all replicates for the linear regression.
 Mapping<java.lang.String,java.lang.Integer> copyMap()
          Copies the content of the Mapping object.
 double evaluate(java.lang.String fasta, int column, java.lang.String uraMeth, java.lang.String printName, java.util.HashMap<java.lang.String,java.lang.Double> corr, boolean plot)
          Method for the Uracil-based evaluation of the values: Compares (average) uracil number of the sequence to logarithm of the ratio.
 void findMiniMaxi()
          Sets the new minimum and maximum
 java.lang.String getAbsent()
          Returns the call used for present/absent filtering.
 java.lang.String getAbsentLabel()
          Returns the name of the column with present/absent calls.
 java.lang.String[] getAttrDescr()
          Returns the description of the attributes.
 java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> getAttributes()
          Returns the attribute lists.
 double getAvgLo()
          Returns the average log(e'/n').
 double getAvgUr()
          Returns the average number of Uracil.
 java.util.HashMap<java.lang.String,java.lang.Double> getCorrNewPre()
          Returns the correction bias values for the ratio newly transcribed/pre-existing.
 java.util.HashMap<java.lang.String,java.lang.Double> getCorrNewTot()
          Returns the correction bias values for the ratio newly transcribed/total.
 java.util.HashMap<java.lang.String,java.lang.Double> getCorrPreTot()
          Returns the correction bias values for the ratio pre-existing/total.
 double[] getDat()
          Returns the evaluated normalized data.
 java.lang.String getFilename()
          Returns the name of the file containing the data.
 java.lang.String getGeneName()
          Returns the name of the column with gene names.
 Mapping<java.lang.String,java.lang.Integer> getMap()
          Returns the map corresponding to the data.
 double getMaximum()
          Returns the maximal expression value present in the data
 int getMethod()
          Returns the number of the method used for ratio calculation.
 double getMinimum()
          Returns the minimal expression value present in the data
 java.lang.String[] getNewDescr()
          Returns the description = column labels of newly transcribed RNA.
 double[][] getNewRNA()
          Returns all the values for newly transcribed RNA.
 int getNumberExperiments()
          Returns the number of measured experiments (not changeable through filtering!).
 java.lang.String getPlotName()
          Returns the name of the file into which evaluation results will be printed as a plottable table.
 double[] getPqs()
          Returns the probe set quality scores.
 java.lang.String[] getPreDescr()
          Returns the description = column labels of pre-existing RNA.
 double[][] getPreRNA()
          Returns all the values for pre-existing RNA.
 int getReplicate()
          Returns the number of the replicate used for calculations.
 int getReplicatesTotal()
          Returns the total number of replicates.
 int getSize()
          Returns the number of probesets present after filtering.
 java.lang.String[] getSpot()
          Returns the list of spots.
 java.lang.String getSpotid()
          Returns the name of the column with probeset ids.
 java.lang.String[] getTotalDescr()
          Returns the description = column labeles of total RNA.
 double[][] getTotalRNA()
          Returns all the values for total RNA.
 boolean isUnequal()
          Returns TRUE if unequal number of RNA measurements has been loaded.
 void loadAttributesFromDatafile(java.util.ArrayList<java.lang.String> newAttributes)
          Loads attributes from original data file.
 void loadAttributesFromDatafile(java.util.ArrayList<java.lang.String> newAttributes, boolean turnReverseMapOff)
          Loads attributes from the original data file.
 void loadData(java.lang.String file, java.util.List<java.lang.String> columnsTotal, java.util.List<java.lang.String> columnsNew, java.util.List<java.lang.String> columnsPre, java.util.List<java.lang.String> attr, boolean log)
          Loads the data from a file.
 void loadPresentCallsFromDatafile(java.util.ArrayList<java.lang.String> presentCallAttributes)
          Loads present calls or other attributes with a small number of values from the original data file.
 void readInput(java.lang.String file, java.util.List<java.lang.String> columnsTotal, java.util.List<java.lang.String> columnsNew, java.util.List<java.lang.String> columnsPre, java.util.List<java.lang.String> addit, boolean log)
          Takes an input file, reads the values and saves them in the class variables of the Data object.
 double[] restrictRatio(double[][] input, int replicate)
          Restricts a multidimensional array onto an array with one dimension containing the wanted replicate, while keeping the order.
 void setAbsent(java.lang.String absent)
          Sets the name of the column (column label) which holds information on present/absent.
 void setAttrDescr(java.lang.String[] attrDescr)
          Sets the description of all attributes.
 void setAttributes(java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> attributes)
          Sets the attributes list for the data.
 void setCorrNewPre(java.util.HashMap<java.lang.String,java.lang.Double> corr)
          Sets the correction bias values for the ratio newly transcribed/pre-existing.
 void setCorrNewTot(java.util.HashMap<java.lang.String,java.lang.Double> corrNewTot)
          Sets the correction bias values for the ratio newly transcribed/total.
 void setCorrPreTot(java.util.HashMap<java.lang.String,java.lang.Double> corrPreTot)
          Sets the correction bias values for the ratio pre-existing/total.
 void setFilename(java.lang.String filename)
          Sets the name of the file holding the data information.
 void setGeneName(java.lang.String geneName)
          Sets the name of the column which holds information on the gene name.
 void setMap(Mapping<java.lang.String,java.lang.Integer> map)
          Sets the mapping corresponding to the whole data and filtered values.
 void setMaximum(double maximum)
          Sets the maximum RNA value
 void setMethod(int i)
          Sets the method used for calculating the average ratios over all replicates.
 void setMinimum(double minimum)
          Sets the minimum RNA value
 void setPqs(double[] pqs)
          Sets the probe set quality scores.
 void setReplicate(int replicate)
          Sets the replicate used for ratio calculations, if method is restricting of ratios to one replicate.
 void setSpotid(java.lang.String probesetId)
          Sets the name of the column with probeset ids.
 void setUnequal(boolean unequal)
          Set the value of the unequal variable, meaning if there is an unequal number of measurements (new, pre, total).
 void writeOutput(java.lang.String output, java.util.List<java.lang.String> columnsTotal, java.util.List<java.lang.String> columnsNew, java.util.List<java.lang.String> columnsPre, java.util.List<java.lang.String> addit)
          Desired columns are written to a file; former order is not kept, instead all values of one type are added sequentially.
 void writeToFileArray(java.lang.String output, double[] array)
          Writes the half-life values contained in the array and in the map together with corresponding spotIds into a file.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

RATIOFIRST

public static final int RATIOFIRST
See Also:
Constant Field Values

AVERAGEFIRST

public static final int AVERAGEFIRST
See Also:
Constant Field Values

REPLICATE

public static final int REPLICATE
See Also:
Constant Field Values

LOGEN

public static final java.lang.String LOGEN
See Also:
Constant Field Values

LOGUN

public static final java.lang.String LOGUN
See Also:
Constant Field Values

LOGEU

public static final java.lang.String LOGEU
See Also:
Constant Field Values

GENEDEFAULT

public static final java.lang.String GENEDEFAULT
See Also:
Constant Field Values
Constructor Detail

Data

public Data(java.lang.String file,
            java.util.List<java.lang.String> columnsTotal,
            java.util.List<java.lang.String> columnsNew,
            java.util.List<java.lang.String> columnsPre,
            boolean log)
Constructs a Data-Object based on an Input-File and the list of columns to be read with no additional attributes.

Parameters:
file - Name of the Input-file
columnsTotal - List containing the labels of columns for total RNA
columnsNew - List containing the labels of columns for newly transcribed RNA
columnsPre - List containing the labels of columns for pre-existing RNA

Data

public Data(java.lang.String file,
            java.util.List<java.lang.String> columnsTotal,
            java.util.List<java.lang.String> columnsNew,
            java.util.List<java.lang.String> columnsPre,
            java.util.List<java.lang.String> attr,
            boolean log)
Constructs a Data-Object based on an Input-File and the list of columns to be read, defines columns containing attributes.

Parameters:
file - Name of the Input-file
columnsTotal - List containing the labels of columns for total RNA
columnsNew - List containing the labels of columns for newly transcribed RNA
columnsPre - List containing the labels of columns for pre-existing RNA
attr - List containing the labels of columns for attributes

Data

public Data()
Constructs an empty Data-Object, so that parameters for data loading can be set before starting.


Data

public Data(double[][] totalRNA,
            double[][] newRNA,
            double[][] preRNA,
            java.lang.String[] totalDescr,
            java.lang.String[] newDescr,
            java.lang.String[] preDescr,
            Mapping<java.lang.String,java.lang.Integer> map)
Constructs a Data-Object based on already existing data.

Parameters:
totalRNA - Array containing all values of total RNA
newRNA - Array containing all values of newly transcribed RNA
preRNA - Array containing all values of pre-existing RNA
totalDescr - A description that matches the columns of the arrays containing the values to the labels of the columns for total RNA
newDescr - matches columns of arrays to labels for newly transcribed RNA
preDescr - matches columns of arrays to labels for pre-existing RNA
map - A Map matching SpotId to index of RNA-arrays, containing only filtered values
Method Detail

loadData

public void loadData(java.lang.String file,
                     java.util.List<java.lang.String> columnsTotal,
                     java.util.List<java.lang.String> columnsNew,
                     java.util.List<java.lang.String> columnsPre,
                     java.util.List<java.lang.String> attr,
                     boolean log)
Loads the data from a file.

Parameters:
file - Name of the Input-file
columnsTotal - List containing the labels of columns for total RNA
columnsNew - List containing the labels of columns for newly transcribed RNA
columnsPre - List containing the labels of columns for pre-existing RNA
attr - List containing the labels of columns for attributes

readInput

public void readInput(java.lang.String file,
                      java.util.List<java.lang.String> columnsTotal,
                      java.util.List<java.lang.String> columnsNew,
                      java.util.List<java.lang.String> columnsPre,
                      java.util.List<java.lang.String> addit,
                      boolean log)
Takes an input file, reads the values and saves them in the class variables of the Data object.

Parameters:
file - Name of the input file
columnsTotal - List containing labels of columns for total RNA
columnsNew - List containing labels of columns for newly transcribed RNA
columnsPre - List containing labels of columns for pre-existing RNA
addit - List containing labels of columns with additional information; null if no additional information is wanted

calculateMappingForAttributes

public void calculateMappingForAttributes(java.lang.String[][] allAttributes,
                                          java.lang.String[] ids)
Transcribes the attributes into a mapping id -> attribute.

Parameters:
allAttributes - A list of attributes for each id
ids - The ids corresponding to the indices

addAttributes

public void addAttributes(java.lang.String inputfile)
Reads in every attribute from a given file.

Parameters:
inputfile - Name of the file that contains attributes

addAttributes

public void addAttributes(java.lang.String inputfile,
                          java.util.ArrayList<java.lang.String> columnLabels)
Reads in regular attributes from a file.

Parameters:
inputfile - Name of the file that contains attributes
columnLabels - Labels of relevant columns

addPresenceCalls

public void addPresenceCalls(java.lang.String inputfile,
                             java.util.ArrayList<java.lang.String> columnLabels)
Reads in attributes from a file. Specific for attributes with a very small number of values (e.g. present calls) to speed up the loading. Please note that with this method the reverse mapping from attribute to list of IDs is not possible.

Parameters:
inputfile - Name of the file that contains attributes
columnLabels - Labels of relevant columns

addAttributes

public void addAttributes(java.lang.String inputfile,
                          java.util.ArrayList<java.lang.String> columnLabels,
                          boolean turnReverseMapOff)
Reads in a file containing several columns, of which one contains the spotID, the others contain attributes. The resulting Mappings are added to the List attrMaps and accessible over the index received from attrMapsDescr, where the name of the column is stored

Parameters:
inputfile - Name of the file that contains attributes
columnLabels - Labels of relevant columns
turnReverseMapOff - TRUE it attributes are present calls or similar attributes with a very small number of values

loadAttributesFromDatafile

public void loadAttributesFromDatafile(java.util.ArrayList<java.lang.String> newAttributes)
Loads attributes from original data file.

Parameters:
newAttributes - The list of attributes that will be loaded

loadPresentCallsFromDatafile

public void loadPresentCallsFromDatafile(java.util.ArrayList<java.lang.String> presentCallAttributes)
Loads present calls or other attributes with a small number of values from the original data file. Please note that reverse mapping (attribute to list of IDs) is not available for attributes loaded with this method for the sake of speed.

Parameters:
presentCallAttributes - The list of attributes that will be loaded

loadAttributesFromDatafile

public void loadAttributesFromDatafile(java.util.ArrayList<java.lang.String> newAttributes,
                                       boolean turnReverseMapOff)
Loads attributes from the original data file.

Parameters:
newAttributes - The list of attributes that will be loaded
turnReverseMapOff - TRUE if attributes are present calls or similar attributes with very few possible values

writeOutput

public void writeOutput(java.lang.String output,
                        java.util.List<java.lang.String> columnsTotal,
                        java.util.List<java.lang.String> columnsNew,
                        java.util.List<java.lang.String> columnsPre,
                        java.util.List<java.lang.String> addit)
Desired columns are written to a file; former order is not kept, instead all values of one type are added sequentially.

Parameters:
output - Name of the output file
columnsTotal - List containing labels of columns for total RNA that shall be exported
columnsNew - List containing labels of columns for newly transcribed RNA that shall be exported
columnsPre - List containing labels of columns for pre-existing RNA that shall be exported
addit - List containing labels of columns for attributes

copyMap

public Mapping<java.lang.String,java.lang.Integer> copyMap()
Copies the content of the Mapping object.

Returns:
copy of the map that maps SpotID to indices

calculateRatio

public double[] calculateRatio(double[][] rna,
                               double[][] total,
                               java.util.HashMap<java.lang.String,java.lang.Double> corr,
                               int replicate)
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. If none specified the default method is 'calculateRatioFirst'. Please perform the filtering method 'filterCorrectionBias' before using this method.

Parameters:
rna - A set of RNA values serving as numerator
total - A second set of RNA values serving as denominator
corr - The map for ID and bias correction, null if no correction should take place
replicate - The number of the replicate (starting from 0) that will be used for method REPLICATE; -1 if average should be calculated
Returns:
The ratio of the two averaged sets of RNA

calculateRatio

public double[] calculateRatio(double[][] rna,
                               double[][] total,
                               java.util.HashMap<java.lang.String,java.lang.Double> corr)
Calculates the ratios for an average over a set of replicates.

Parameters:
rna - A set of RNA values serving as numerator
total - A second set of RNA values serving as denominator
corr - The map for ID and bias correction, null if no correction should take place
Returns:
The ratio of the two averaged sets of RNA

calculateNewMapping

public Mapping<java.lang.String,java.lang.Integer> calculateNewMapping()
Calculates the Mapping corresponding to the ratio.

Returns:
Mapping which matches SpotID to index of ratio array

restrictRatio

public double[] restrictRatio(double[][] input,
                              int replicate)
Restricts a multidimensional array onto an array with one dimension containing the wanted replicate, while keeping the order.

Parameters:
input - Ratio or half-life array
replicate - The replicate to which the ratio will be restricted
Returns:
single dimensional array

calculateRatioFirst

public double[] calculateRatioFirst(double[][] allRatio)
calculates the average values from all replicates for the linear regression. calculates the average of the ratios (RATIOFIRST method)

Parameters:
allRatio - The array containing the previously calculated ratios
Returns:
The average of the different ratios

calculateAverageFirst

public double[] calculateAverageFirst(double[][] rna,
                                      double[][] total,
                                      java.util.HashMap<java.lang.String,java.lang.Double> corr)
Calculates the average values from all replicates for the linear regression through calculating the ratio of the averages (AVERAGEFIRST method).

Parameters:
rna - A set of RNA that serves as numerator
total - A set of RNA that serves as denominator
corr - The map for ID and bias correction, null if no correction should take place
Returns:
The ratio of the averages of the given sets

writeToFileArray

public void writeToFileArray(java.lang.String output,
                             double[] array)
Writes the half-life values contained in the array and in the map together with corresponding spotIds into a file. Appropriate for half-lives, ratios & pqs (for which the new mapping applies)

Parameters:
output - Name of output file
array - List containing any set of values

evaluate

public double evaluate(java.lang.String fasta,
                       int column,
                       java.lang.String uraMeth,
                       java.lang.String printName,
                       java.util.HashMap<java.lang.String,java.lang.Double> corr,
                       boolean plot)
Method for the Uracil-based evaluation of the values: Compares (average) uracil number of the sequence to logarithm of the ratio. For multiple transcript entries per gene an average uracil number is calculated.

Parameters:
fasta - The fasta file which contains the sequences
column - The number of the column (starting with 1) of the header in which the genename is contained (i.e. header: > genename | attribute | attribute leads to column = 1)
uraMeth - Either "log(e'/n')", or "log(e'/u')", or "log(u'/n')", according to the ratio which will be evaluated
printName - Name of the output file for plotting information
corr - The map for ID and bias correction, null if no correction should take place
plot - TRUE if histogram plot is wanted, FALSE otherwise
Returns:
result Average uracil number

findMiniMaxi

public void findMiniMaxi()
Sets the new minimum and maximum


setCorrNewPre

public void setCorrNewPre(java.util.HashMap<java.lang.String,java.lang.Double> corr)
Sets the correction bias values for the ratio newly transcribed/pre-existing.

Parameters:
corr - The correction bias values for the ratio newly transcribed/pre-existing

setCorrNewTot

public void setCorrNewTot(java.util.HashMap<java.lang.String,java.lang.Double> corrNewTot)
Sets the correction bias values for the ratio newly transcribed/total.

Parameters:
corrNewTot - The correction bias values for the ratio newly transcribed/total

setCorrPreTot

public void setCorrPreTot(java.util.HashMap<java.lang.String,java.lang.Double> corrPreTot)
Sets the correction bias values for the ratio pre-existing/total.

Parameters:
corrPreTot - The correction bias values for the ratio pre-existing/total

setMethod

public void setMethod(int i)
Sets the method used for calculating the average ratios over all replicates.

Parameters:
i - The integer value for the method

setMap

public void setMap(Mapping<java.lang.String,java.lang.Integer> map)
Sets the mapping corresponding to the whole data and filtered values.

Parameters:
map - The mapping corresponding to data

setMaximum

public void setMaximum(double maximum)
Sets the maximum RNA value

Parameters:
maximum - Maximum RNA value

setMinimum

public void setMinimum(double minimum)
Sets the minimum RNA value

Parameters:
minimum - Minimum RNA value

setFilename

public void setFilename(java.lang.String filename)
Sets the name of the file holding the data information.

Parameters:
filename - Name of the file with the data

setAttributes

public void setAttributes(java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> attributes)
Sets the attributes list for the data.

Parameters:
attributes - The list of attribute mappings

setAttrDescr

public void setAttrDescr(java.lang.String[] attrDescr)
Sets the description of all attributes.

Parameters:
attrDescr - The description of attributes

setAbsent

public void setAbsent(java.lang.String absent)
Sets the name of the column (column label) which holds information on present/absent.

Parameters:
absent - Column label for present/absent calls

setGeneName

public void setGeneName(java.lang.String geneName)
Sets the name of the column which holds information on the gene name.

Parameters:
geneName - Column label for gene name

setSpotid

public void setSpotid(java.lang.String probesetId)
Sets the name of the column with probeset ids.

Parameters:
probesetId - Name of the column with probeset ids

setUnequal

public void setUnequal(boolean unequal)
Set the value of the unequal variable, meaning if there is an unequal number of measurements (new, pre, total).

Parameters:
unequal - True, if there is an unequal number of measurements

setReplicate

public void setReplicate(int replicate)
Sets the replicate used for ratio calculations, if method is restricting of ratios to one replicate.

Parameters:
replicate - The replicate used for ratio calculations

setPqs

public void setPqs(double[] pqs)
Sets the probe set quality scores.

Parameters:
pqs - The probe set quality scores

getPqs

public double[] getPqs()
Returns the probe set quality scores.

Returns:
The probe set quality scores

getAbsent

public java.lang.String getAbsent()
Returns the call used for present/absent filtering.

Returns:
The call used for present/absent filtering

getMethod

public int getMethod()
Returns the number of the method used for ratio calculation.

Returns:
Number of the method used for ratio calculation

getReplicate

public int getReplicate()
Returns the number of the replicate used for calculations.

Returns:
Number of the replicate used for calculations

getAbsentLabel

public java.lang.String getAbsentLabel()
Returns the name of the column with present/absent calls.

Returns:
The name of the column with present/absent calls

getGeneName

public java.lang.String getGeneName()
Returns the name of the column with gene names.

Returns:
The name of the column with gene names

getSpotid

public java.lang.String getSpotid()
Returns the name of the column with probeset ids.

Returns:
The name of the column with probeset ids

getMaximum

public double getMaximum()
Returns the maximal expression value present in the data

Returns:
The maximal expression value

getMinimum

public double getMinimum()
Returns the minimal expression value present in the data

Returns:
The minimal expression value

getFilename

public java.lang.String getFilename()
Returns the name of the file containing the data.

Returns:
The name of the data file

getSpot

public java.lang.String[] getSpot()
Returns the list of spots.

Returns:
The list of spots

getDat

public double[] getDat()
Returns the evaluated normalized data.

Returns:
The evaluated normalized data

getAttributes

public java.util.ArrayList<Mapping<java.lang.String,java.lang.String>> getAttributes()
Returns the attribute lists.

Returns:
The list of attribute mappings

getMap

public Mapping<java.lang.String,java.lang.Integer> getMap()
Returns the map corresponding to the data.

Returns:
The map for the data

getAttrDescr

public java.lang.String[] getAttrDescr()
Returns the description of the attributes.

Returns:
The description of attributes

getNewDescr

public java.lang.String[] getNewDescr()
Returns the description = column labels of newly transcribed RNA.

Returns:
The description of newly transcribed RNA

getNewRNA

public double[][] getNewRNA()
Returns all the values for newly transcribed RNA.

Returns:
The measured values for newly transcribed RNA

getCorrNewPre

public java.util.HashMap<java.lang.String,java.lang.Double> getCorrNewPre()
Returns the correction bias values for the ratio newly transcribed/pre-existing.

Returns:
The correction bias values for the ratio newly transcribed/pre-existing

getCorrNewTot

public java.util.HashMap<java.lang.String,java.lang.Double> getCorrNewTot()
Returns the correction bias values for the ratio newly transcribed/total.

Returns:
The correction bias values for the ratio newly transcribed/total

getCorrPreTot

public java.util.HashMap<java.lang.String,java.lang.Double> getCorrPreTot()
Returns the correction bias values for the ratio pre-existing/total.

Returns:
The correction bias values for the ratio pre-existing/total

getPreDescr

public java.lang.String[] getPreDescr()
Returns the description = column labels of pre-existing RNA.

Returns:
The description of pre-existing RNA

getPreRNA

public double[][] getPreRNA()
Returns all the values for pre-existing RNA.

Returns:
The measured values for pre-existing RNA

getTotalDescr

public java.lang.String[] getTotalDescr()
Returns the description = column labeles of total RNA.

Returns:
The description of total RNA

getTotalRNA

public double[][] getTotalRNA()
Returns all the values for total RNA.

Returns:
The measured values for total RNA

getNumberExperiments

public int getNumberExperiments()
Returns the number of measured experiments (not changeable through filtering!).

Returns:
The number of measured experiments

getSize

public int getSize()
Returns the number of probesets present after filtering.

Returns:
The number of (filtered) probesets

getAvgLo

public double getAvgLo()
Returns the average log(e'/n').

Returns:
The average log(e'/n')

getAvgUr

public double getAvgUr()
Returns the average number of Uracil.

Returns:
The average number of Uracil

getReplicatesTotal

public int getReplicatesTotal()
Returns the total number of replicates.

Returns:
The total number of replicates

getPlotName

public java.lang.String getPlotName()
Returns the name of the file into which evaluation results will be printed as a plottable table.

Returns:
The name of the file containing the plot information for evaluation

isUnequal

public boolean isUnequal()
Returns TRUE if unequal number of RNA measurements has been loaded.

Returns:
TRUE if unequal number of RNA measurements has been loaded