Man pages for Bioconductor-mirror/cn.mops
cn.mops - Mixture of Poissons for CNV detection in NGS data

calcFractionalCopyNumbersCalculation of fractional copy numbers for the CNVs and CNV...
calcFractionalCopyNumbers-CNVDetectionResult-methodCalculation of fractional copy numbers for the CNVs and CNV...
calcIntegerCopyNumbersCalculation of integer copy numbers for the CNVs and CNV...
calcIntegerCopyNumbers-CNVDetectionResult-methodCalculation of integer copy numbers for the CNVs and CNV...
cn.mopsCopy number detection in NGS data.
CNVDetectionResultClass "CNVDetectionResult"
cnvrThis generic function returns CNV regions of a CNV detection...
CNVRangesGenomic locations and indices of the simulated CNVs.
cnvr-CNVDetectionResult-methodThis generic function returns CNV regions of a CNV detection...
cnvsThis generic function returns CNVs of a CNV detection method...
cnvs-CNVDetectionResult-methodThis generic function returns CNVs of a CNV detection method...
exomecn.mopsCopy number detection in exome sequencing data.
exomeCountsRead counts from exome sequencing for CNV detection
getReadCountsFromBAMCalculation of read counts from BAM files.
getSegmentReadCountsFromBAMCalculation of read counts from BAM files for predefined...
grThis generic function returns the genomic ranges of a CNV...
gr-CNVDetectionResult-methodThis generic function returns the genomic ranges of a CNV...
haplocn.mopsCopy number detection in NGS data of haploid samples.
individualCallThis generic function returns the individual calls of a CNV...
individualCall-CNVDetectionResult-methodThis generic function returns the individual calls of a CNV...
iniCallThis generic function returns the informative/non-informative...
iniCall-CNVDetectionResult-methodThis generic function returns the informative/non-informative...
integerCopyNumberThis generic function returns the integer copy numbers of a...
integerCopyNumber-CNVDetectionResult-methodThis generic function returns the integer copy numbers of a...
localAssessmentsThis generic function returns the local assessments, i.e....
localAssessments-CNVDetectionResult-methodThis generic function returns the local assessments, i.e....
makeRobustCNVRCalculates robust CNV regions.
normalizeChromosomesNormalization of NGS data.
normalizedDataThis generic function returns the normalized data of a CNV...
normalizedData-CNVDetectionResult-methodThis generic function returns the normalized data of a CNV...
normalizeGenomeNormalization of NGS data
paramsThis generic function returns the parameters of a CNV...
params-CNVDetectionResult-methodThis generic function returns the parameters of a CNV...
plotPlots a CNVDetectionResult
posteriorProbsThis generic function returns the posterior probabilities of...
posteriorProbs-CNVDetectionResult-methodThis generic function returns the posterior probabilities of...
referencecn.mopsCopy number detection in NGS data with in a control versus...
sampleNamesThis generic function returns the sample names of a CNV...
sampleNames-CNVDetectionResult-methodThis generic function returns the sample names of a CNV...
segmentFast segmentation of CNV calls.
segmentationThis generic function returns segmentation of a CNV detection...
segmentation-CNVDetectionResult-methodThis generic function returns segmentation of a CNV detection...
segplotVisualization of a CNV detection result.
segplot-CNVDetectionResult-methodVisualization of a CNV detection result.
showDisplays the result object of a copy number detection method.
singlecn.mopsCopy number detection in NGS data with in a setting in which...
XA simulated data set for CNV detection from NGS data.
XRangesA simulated data set for CNV detection from NGS data.
Bioconductor-mirror/cn.mops documentation built on June 1, 2017, 6:35 a.m.