Package: cn.mops 1.51.0

Gundula Povysil

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

cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.

Authors:Guenter Klambauer [aut], Gundula Povysil [cre]

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cn.mops/json (API)

# Install 'cn.mops' in R:
install.packages('cn.mops', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • CNVRanges - Genomic locations and indices of the simulated CNVs.
  • X - A simulated data set for CNV detection from NGS data.
  • XRanges - A simulated data set for CNV detection from NGS data.
  • exomeCounts - Read counts from exome sequencing for CNV detection

On BioConductor:cn.mops-1.51.0(bioc 3.20)cn.mops-1.50.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

27 exports 1.95 score 32 dependencies 4 dependents 8 mentions

Last updated 2 months agofrom:ee78d2ead0

Exports:calcFractionalCopyNumberscalcIntegerCopyNumberscn.mopscnvrcnvsexomecn.mopsgetReadCountsFromBAMgetSegmentReadCountsFromBAMgrhaplocn.mopsindividualCalliniCallintegerCopyNumberlocalAssessmentsmakeRobustCNVRnormalizeChromosomesnormalizedDatanormalizeGenomeparamsposteriorProbsreferencecn.mopssampleNamessegmentsegmentationsegplotshowsinglecn.mops

Dependencies:askpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rmimeopensslR6RhtslibRsamtoolsS4VectorssnowsysUCSC.utilsXVectorzlibbioc

cn.mops: Manual for the R package

Rendered fromcn.mops.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2020-06-04
Started: 2012-10-16

Readme and manuals

Help Manual

Help pageTopics
Calculation of fractional copy numbers for the CNVs and CNV regions.calcFractionalCopyNumbers
Calculation of fractional copy numbers for the CNVs and CNV regions.calcFractionalCopyNumbers,CNVDetectionResult-method
Calculation of integer copy numbers for the CNVs and CNV regions.calcIntegerCopyNumbers
Calculation of integer copy numbers for the CNVs and CNV regions.calcIntegerCopyNumbers,CNVDetectionResult-method
Copy number detection in NGS data.cn.mops
Class "CNVDetectionResult"CNVDetectionResult CnvDetectionResult cnvdetectionresult CNVDetectionResult-class
This generic function returns CNV regions of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.cnvr
This generic function returns CNV regions of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.cnvr,CNVDetectionResult-method
Genomic locations and indices of the simulated CNVs.CNVRanges
This generic function returns CNVs of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.cnvs
This generic function returns CNVs of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.cnvs,CNVDetectionResult-method
Copy number detection in exome sequencing data.exomecn.mops
Read counts from exome sequencing for CNV detectionexomeCounts
Calculation of read counts from BAM files.getReadCountsFromBAM
Calculation of read counts from BAM files for predefined segments.getSegmentReadCountsFromBAM
This generic function returns the genomic ranges of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.gr
This generic function returns the genomic ranges of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.gr,CNVDetectionResult-method
Copy number detection in NGS data of haploid samples.haplocn.mops
This generic function returns the individual calls of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.individualCall
This generic function returns the individual calls of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.individualCall,CNVDetectionResult-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).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,CNVDetectionResult-method
This generic function returns the integer copy numbers of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.integerCopyNumber
This generic function returns the integer copy numbers of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.integerCopyNumber,CNVDetectionResult-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.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,CNVDetectionResult-method
Calculates robust CNV regions.makeRobustCNVR makeRobustCNVR,CNVDetectionResult-method
Normalization of NGS data.normalizeChromosomes
This generic function returns the normalized data of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.normalizedData
This generic function returns the normalized data of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.normalizedData,CNVDetectionResult-method
Normalization of NGS datanormalizeGenome
This generic function returns the parameters of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.params
This generic function returns the parameters of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.params,CNVDetectionResult-method
Plots a CNVDetectionResultplot,CNVDetectionResult,missing-method plot-methods
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
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,CNVDetectionResult-method
Copy number detection in NGS data with in a control versus cases setting.referencecn.mops
This generic function returns the sample names of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.sampleNames
This generic function returns the sample names of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.sampleNames,CNVDetectionResult-method
Fast segmentation of CNV calls.segment
This generic function returns segmentation of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.segmentation
This generic function returns segmentation of a CNV detection method stored in an instance of 'CNVDetectionResult-class'.segmentation,CNVDetectionResult-method
Visualization of a CNV detection result.segplot
Visualization of a CNV detection result.segplot,CNVDetectionResult-method
Displays the result object of a copy number detection method.show,CNVDetectionResult-method show-methods
Copy number detection in NGS data with in a setting in which only one sample is availablesinglecn.mops
A simulated data set for CNV detection from NGS data.X
A simulated data set for CNV detection from NGS data.XRanges