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

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Documentation for package ‘cn.mops’ version 1.38.0

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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.