Man pages for gpovysil/cn.mops
cn.mops - Mixture of Poissons for CNV detection in NGS data
| calcFractionalCopyNumbers | Calculation of fractional copy numbers for the CNVs and CNV... |
| calcFractionalCopyNumbers-CNVDetectionResult-method | Calculation of fractional copy numbers for the CNVs and CNV... |
| calcIntegerCopyNumbers | Calculation of integer copy numbers for the CNVs and CNV... |
| calcIntegerCopyNumbers-CNVDetectionResult-method | Calculation of integer copy numbers for the CNVs and CNV... |
| cn.mops | Copy number detection in NGS data. |
| CNVDetectionResult | Class "CNVDetectionResult" |
| cnvr | This generic function returns CNV regions of a CNV detection... |
| CNVRanges | Genomic locations and indices of the simulated CNVs. |
| cnvr-CNVDetectionResult-method | This generic function returns CNV regions of a CNV detection... |
| cnvs | This generic function returns CNVs of a CNV detection method... |
| cnvs-CNVDetectionResult-method | This generic function returns CNVs of a CNV detection method... |
| 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... |
| gr | This generic function returns the genomic ranges of a CNV... |
| gr-CNVDetectionResult-method | This generic function returns the genomic ranges of a CNV... |
| haplocn.mops | Copy number detection in NGS data of haploid samples. |
| individualCall | This generic function returns the individual calls of a CNV... |
| individualCall-CNVDetectionResult-method | This generic function returns the individual calls of a CNV... |
| iniCall | This generic function returns the informative/non-informative... |
| iniCall-CNVDetectionResult-method | This generic function returns the informative/non-informative... |
| integerCopyNumber | This generic function returns the integer copy numbers of a... |
| integerCopyNumber-CNVDetectionResult-method | This generic function returns the integer copy numbers of a... |
| localAssessments | This generic function returns the local assessments, i.e.... |
| localAssessments-CNVDetectionResult-method | This generic function returns the local assessments, i.e.... |
| makeRobustCNVR | Calculates robust CNV regions. |
| normalizeChromosomes | Normalization of NGS data. |
| normalizedData | This generic function returns the normalized data of a CNV... |
| normalizedData-CNVDetectionResult-method | This generic function returns the normalized data of a CNV... |
| normalizeGenome | Normalization of NGS data |
| params | This generic function returns the parameters of a CNV... |
| params-CNVDetectionResult-method | This generic function returns the parameters of a CNV... |
| plot | Plots a CNVDetectionResult |
| posteriorProbs | This generic function returns the posterior probabilities of... |
| posteriorProbs-CNVDetectionResult-method | This generic function returns the posterior probabilities of... |
| referencecn.mops | Copy number detection in NGS data with in a control versus... |
| sampleNames | This generic function returns the sample names of a CNV... |
| sampleNames-CNVDetectionResult-method | This generic function returns the sample names of a CNV... |
| segment | Fast segmentation of CNV calls. |
| segmentation | This generic function returns segmentation of a CNV detection... |
| segmentation-CNVDetectionResult-method | This generic function returns segmentation of a CNV detection... |
| segplot | Visualization of a CNV detection result. |
| segplot-CNVDetectionResult-method | Visualization of a CNV detection result. |
| show | Displays the result object of a copy number detection method. |
| singlecn.mops | Copy number detection in NGS data with in a setting in which... |
| X | A simulated data set for CNV detection from NGS data. |
| XRanges | A simulated data set for CNV detection from NGS data. |
