A B C D E F G H I K L M N O P R S T U V

C

calculateExpectedValues(ArrayList<String>, int) - Static method in class Exon

Computes the expected value for each exon by average the values in the baseline files

calculateNormalizationFactor(ArrayList<String>, int) - Static method in class Exon

Deprecated

calculateSNPPositions(Exon, MappedReads) - Static method in class Exon

Calculated the positions of the SNPs

calculateStdDevValues(ArrayList<String>, int, ArrayList<Exon>) - Static method in class Exon

Computes the std deviation values for each exon by average the values in the baseline files

chr - Variable in class Exon

chr - Variable in class Expression

chr - Variable in class MappedReads

chromosome - Variable in class Pileup

chromosomes - Static variable in class CONDR

chromosomes - Static variable in class ConvertToExonFormat

chromosomes - Static variable in class CreateExonFile

chromosomes - Static variable in class PileupToExon

chromosomes - Static variable in class SimulateExonMeasurements

CNV - Class in <Unnamed>

Class to compute where the CNVs are.

CNV(int) - Constructor for class CNV

computeAtRunTime - Static variable in class State

computeBackwardProbabilities(ArrayList<Exon>, ArrayList<Exon>, ArrayList<Exon>, int, Gamma, double, double, double, double) - Static method in class HiddenMarkovModel

Computes the backward probabilities for the observation

computeForwardProbabilities(ArrayList<Exon>, ArrayList<Exon>, ArrayList<Exon>, int, Gamma, double, double, double, double) - Static method in class HiddenMarkovModel

Computes the forward probabilities for the observation

CONDR - Class in <Unnamed>

Main calling function of program Gets data; parses it; computes most likely states

CONDR() - Constructor for class CONDR

containsPosition(int) - Method in class Exon

Does this exon contain the specified genomic position?

ConvertToExonFormat - Class in <Unnamed>

File Format of output (tab delimited) chromosome exonStart exonEnd geneName FPKM/coverage SNP levels/BAF .pileup -> .exon

ConvertToExonFormat() - Constructor for class ConvertToExonFormat

coverage - Variable in class MappedReads

coverage - Variable in class Pileup

CreateExonFile - Class in <Unnamed>

CreateExonFile() - Constructor for class CreateExonFile