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


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Documentation for package ‘cn.mops’ version 1.6.7

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calcIntegerCopyNumbers Calculation of integer copy numbers for the CNVs and CNV regions.
calcIntegerCopyNumbers-method Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
integerCopyNumber This generic function returns the integer copy numbers of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.
integerCopyNumber-method Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
makeRobustCNVR Calculates robust CNV regions.
makeRobustCNVR-method Class "CNVDetectionResult"
normalizeChromosomes Normalization of NGS data. Normalize quantitative NGS data in order to make counts comparable over samples, i.e., correcting for different library sizes or coverages. Scales each samples' reads such that the coverage is even for all samples after normalization.
normalizedData This generic function returns the normalized data of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.
normalizedData-method Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
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 Class "CNVDetectionResult"
segplot Visualization of a CNV detection result.
segplot-method Class "CNVDetectionResult"
show-method Displays the result object of a copy number detection method.
show-methods Displays the result object of a copy number detection method.
X A simulated data set for CNV detection from NGS data.
XRanges A simulated data set for CNV detection from NGS data.