# cn.mops - Mixture of Poissons for CNV detection in NGS data

## Documentation for package ‘cn.mops’ version 1.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.