| calcFractionalCopyNumbers | Calculation of fractional copy numbers for the CNVs and CNV regions. |
| calcFractionalCopyNumbers-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-method | Calculation of integer copy numbers for the CNVs and CNV regions. |
| cn.mops | Copy number detection in NGS data. |
| CNVDetectionResult | Class "CNVDetectionResult" |
| CnvDetectionResult | Class "CNVDetectionResult" |
| cnvdetectionresult | Class "CNVDetectionResult" |
| CNVDetectionResult-class | Class "CNVDetectionResult" |
| cnvr | This generic function returns CNV regions of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
| cnvr-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-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-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-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-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-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-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. |
| makeRobustCNVR-method | 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-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-method | This generic function returns the parameters of a CNV detection method stored in an instance of 'CNVDetectionResult-class'. |
| plot-method | Plots a CNVDetectionResult |
| 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-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-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-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-method | Visualization of a CNV detection result. |
| show-method | Displays the result object of a copy number detection method. |
| 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. |