calcFractionalCopyNumbers
                        Calculation of fractional copy numbers for the
                        CNVs and CNV regions.
calcFractionalCopyNumbers,CNVDetectionResult-method
                        Calculation of fractional copy numbers for the
                        CNVs and CNV regions.
calcIntegerCopyNumbers
                        Calculation of integer copy numbers for the
                        CNVs and CNV regions.
calcIntegerCopyNumbers,CNVDetectionResult-method
                        Calculation of integer copy numbers for the
                        CNVs and CNV regions.
cn.mops                 Copy number detection in NGS data.
CNVDetectionResult-class
                        Class "CNVDetectionResult"
cnvr                    This generic function returns CNV regions of a
                        CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
cnvr,CNVDetectionResult-method
                        This generic function returns CNV regions of a
                        CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
CNVRanges               Genomic locations and indices of the simulated
                        CNVs.
cnvs                    This generic function returns CNVs of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'.
cnvs,CNVDetectionResult-method
                        This generic function returns CNVs of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'.
exomecn.mops            Copy number detection in exome sequencing data.
exomeCounts             Read counts from exome sequencing for CNV
                        detection
getReadCountsFromBAM    Calculation of read counts from BAM files.
getSegmentReadCountsFromBAM
                        Calculation of read counts from BAM files for
                        predefined segments.
gr                      This generic function returns the genomic
                        ranges of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
gr,CNVDetectionResult-method
                        This generic function returns the genomic
                        ranges of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
haplocn.mops            Copy number detection in NGS data of haploid
                        samples.
individualCall          This generic function returns the individual
                        calls of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
individualCall,CNVDetectionResult-method
                        This generic function returns the individual
                        calls of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
iniCall                 This generic function returns the
                        informative/non-informative call of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'.  The I/NI call is a
                        measure for a genomic segment across all
                        samples, whether this segment is a CNV region
                        (informative) or a normal genomic region
                        (non-informative).
iniCall,CNVDetectionResult-method
                        This generic function returns the
                        informative/non-informative call of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'.  The I/NI call is a
                        measure for a genomic segment across all
                        samples, whether this segment is a CNV region
                        (informative) or a normal genomic region
                        (non-informative).
integerCopyNumber       This generic function returns the integer copy
                        numbers of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
integerCopyNumber,CNVDetectionResult-method
                        This generic function returns the integer copy
                        numbers of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
localAssessments        This generic function returns the local
                        assessments, i.e. signed individual
                        informative/non-informative calls, of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'. For other CNV
                        detection methods this can be (log-) ratios or
                        z-scores.
localAssessments,CNVDetectionResult-method
                        This generic function returns the local
                        assessments, i.e.  signed individual
                        informative/non-informative calls, of a CNV
                        detection method stored in an instance of
                        'CNVDetectionResult-class'. For other CNV
                        detection methods this can be (log-) ratios or
                        z-scores.
makeRobustCNVR          Calculates robust CNV regions.
normalizeChromosomes    Normalization of NGS data.
normalizedData          This generic function returns the normalized
                        data of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
normalizedData,CNVDetectionResult-method
                        This generic function returns the normalized
                        data of a CNV detection method stored in an
                        instance of 'CNVDetectionResult-class'.
normalizeGenome         Normalization of NGS data
params                  This generic function returns the parameters of
                        a CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
params,CNVDetectionResult-method
                        This generic function returns the parameters of
                        a CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
plot-methods            Plots a CNVDetectionResult
posteriorProbs          This generic function returns the posterior
                        probabilities of a CNV detection method stored
                        in an instance of 'CNVDetectionResult-class'.
                        The posterior probabilities are represented as
                        a three dimensional array, where the three
                        dimensions are segment, copy number and
                        individual.
posteriorProbs,CNVDetectionResult-method
                        This generic function returns the posterior
                        probabilities of a CNV detection method stored
                        in an instance of 'CNVDetectionResult-class'.
                        The posterior probabilities are represented as
                        a three dimensional array, where the three
                        dimensions are segment, copy number and
                        individual.
referencecn.mops        Copy number detection in NGS data with in a
                        control versus cases setting.
sampleNames             This generic function returns the sample names
                        of a CNV detection method stored in an instance
                        of 'CNVDetectionResult-class'.
sampleNames,CNVDetectionResult-method
                        This generic function returns the sample names
                        of a CNV detection method stored in an instance
                        of 'CNVDetectionResult-class'.
segment                 Fast segmentation of CNV calls.
segmentation            This generic function returns segmentation of a
                        CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
segmentation,CNVDetectionResult-method
                        This generic function returns segmentation of a
                        CNV detection method stored in an instance of
                        'CNVDetectionResult-class'.
segplot                 Visualization of a CNV detection result.
segplot,CNVDetectionResult-method
                        Visualization of a CNV detection result.
show-methods            Displays the result object of a copy number
                        detection method.
singlecn.mops           Copy number detection in NGS data with in a
                        setting in which only one sample is available
X                       A simulated data set for CNV detection from NGS
                        data.
XRanges                 A simulated data set for CNV detection from NGS
                        data.
