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++.

AuthorGuenter Klambauer
Date of publicationNone
MaintainerGuenter Klambauer <cn.mops@bioinf.jku.at>
LicenseLGPL (>= 2.0)
Version1.20.1
http://www.bioinf.jku.at/software/cnmops/cnmops.html

View on Bioconductor

Man pages

calcFractionalCopyNumbers: Calculation of fractional copy numbers for the CNVs and CNV...

calcFractionalCopyNumbers-CNVDetectionResult-method: Calculation of fractional copy numbers for the CNVs and CNV...

calcIntegerCopyNumbers: Calculation of integer copy numbers for the CNVs and CNV...

calcIntegerCopyNumbers-CNVDetectionResult-method: Calculation of integer copy numbers for the CNVs and CNV...

cn.mops: Copy number detection in NGS data.

CNVDetectionResult: Class "CNVDetectionResult"

cnvr: This generic function returns CNV regions of a CNV detection...

CNVRanges: Genomic locations and indices of the simulated CNVs.

cnvr-CNVDetectionResult-method: This generic function returns CNV regions of a CNV detection...

cnvs: This generic function returns CNVs of a CNV detection method...

cnvs-CNVDetectionResult-method: This generic function returns CNVs of a CNV detection method...

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...

gr: This generic function returns the genomic ranges of a CNV...

gr-CNVDetectionResult-method: This generic function returns the genomic ranges of a CNV...

haplocn.mops: Copy number detection in NGS data of haploid samples.

individualCall: This generic function returns the individual calls of a CNV...

individualCall-CNVDetectionResult-method: This generic function returns the individual calls of a CNV...

iniCall: This generic function returns the informative/non-informative...

iniCall-CNVDetectionResult-method: This generic function returns the informative/non-informative...

integerCopyNumber: This generic function returns the integer copy numbers of a...

integerCopyNumber-CNVDetectionResult-method: This generic function returns the integer copy numbers of a...

localAssessments: This generic function returns the local assessments, i.e....

localAssessments-CNVDetectionResult-method: This generic function returns the local assessments, i.e....

makeRobustCNVR: Calculates robust CNV regions.

normalizeChromosomes: Normalization of NGS data.

normalizedData: This generic function returns the normalized data of a CNV...

normalizedData-CNVDetectionResult-method: This generic function returns the normalized data of a CNV...

normalizeGenome: Normalization of NGS data

params: This generic function returns the parameters of a CNV...

params-CNVDetectionResult-method: This generic function returns the parameters of a CNV...

plot: Plots a CNVDetectionResult

posteriorProbs: This generic function returns the posterior probabilities of...

posteriorProbs-CNVDetectionResult-method: This generic function returns the posterior probabilities of...

referencecn.mops: Copy number detection in NGS data with in a control versus...

sampleNames: This generic function returns the sample names of a CNV...

sampleNames-CNVDetectionResult-method: This generic function returns the sample names of a CNV...

segment: Fast segmentation of CNV calls.

segmentation: This generic function returns segmentation of a CNV detection...

segmentation-CNVDetectionResult-method: This generic function returns segmentation of a CNV detection...

segplot: Visualization of a CNV detection result.

segplot-CNVDetectionResult-method: Visualization of a CNV detection result.

show: Displays the result object of a copy number detection method.

singlecn.mops: Copy number detection in NGS data with in a setting in which...

X: A simulated data set for CNV detection from NGS data.

XRanges: A simulated data set for CNV detection from NGS data.

Functions

calcFractionalCopyNumbers Man page
calcFractionalCopyNumbers,CNVDetectionResult-method Man page
calcFractionalCopyNumbers,CNVDetectionResult-method Man page
calcIntegerCopyNumbers Man page
calcIntegerCopyNumbers,CNVDetectionResult-method Man page
calcIntegerCopyNumbers,CNVDetectionResult-method Man page
cn.mops Man page
cnvdetectionresult Man page
CnvDetectionResult Man page
CNVDetectionResult Man page
CNVDetectionResult-class Man page
CNVDetectionResult-class Man page
cnvr Man page
CNVRanges Man page
cnvr,CNVDetectionResult-method Man page
cnvr,CNVDetectionResult-method Man page
cnvs Man page
cnvs,CNVDetectionResult-method Man page
cnvs,CNVDetectionResult-method Man page
exomecn.mops Man page
exomeCounts Man page
getReadCountsFromBAM Man page
getSegmentReadCountsFromBAM Man page
gr Man page
gr,CNVDetectionResult-method Man page
gr,CNVDetectionResult-method Man page
haplocn.mops Man page
individualCall Man page
individualCall,CNVDetectionResult-method Man page
individualCall,CNVDetectionResult-method Man page
iniCall Man page
iniCall,CNVDetectionResult-method Man page
iniCall,CNVDetectionResult-method Man page
integerCopyNumber Man page
integerCopyNumber,CNVDetectionResult-method Man page
integerCopyNumber,CNVDetectionResult-method Man page
localAssessments Man page
localAssessments,CNVDetectionResult-method Man page
localAssessments,CNVDetectionResult-method Man page
makeRobustCNVR Man page
makeRobustCNVR,CNVDetectionResult-method Man page
makeRobustCNVR,CNVDetectionResult-method Man page
normalizeChromosomes Man page
normalizedData Man page
normalizedData,CNVDetectionResult-method Man page
normalizedData,CNVDetectionResult-method Man page
normalizeGenome Man page
params Man page
params,CNVDetectionResult-method Man page
params,CNVDetectionResult-method Man page
plot,CNVDetectionResult,missing-method Man page
plot-methods Man page
posteriorProbs Man page
posteriorProbs,CNVDetectionResult-method Man page
posteriorProbs,CNVDetectionResult-method Man page
referencecn.mops Man page
sampleNames Man page
sampleNames,CNVDetectionResult-method Man page
sampleNames,CNVDetectionResult-method Man page
segment Man page
segmentation Man page
segmentation,CNVDetectionResult-method Man page
segmentation,CNVDetectionResult-method Man page
segplot Man page
segplot,CNVDetectionResult-method Man page
segplot,CNVDetectionResult-method Man page
show,CNVDetectionResult-method Man page
show-methods Man page
singlecn.mops Man page
X Man page
XRanges Man page

Files

cn.mops/DESCRIPTION
cn.mops/NAMESPACE
cn.mops/R
cn.mops/R/AllClasses.R cn.mops/R/AllGenerics.R cn.mops/R/calcFractionalCopyNumbers.R cn.mops/R/calcIntegerCopyNumbers.R cn.mops/R/cn.mops.R cn.mops/R/exomecn.mops.R cn.mops/R/getReadCountsFromBAM.R cn.mops/R/getSegmentReadCountsFromBAM.R cn.mops/R/haplocn.mops.R cn.mops/R/makeRobustCNVR.R cn.mops/R/methodsAccess.R cn.mops/R/normalizeChromosomes.R cn.mops/R/normalizeGenome.R cn.mops/R/plot-methods.R cn.mops/R/referencecn.mops.R cn.mops/R/segPlot.R cn.mops/R/segment.R cn.mops/R/show-methods.R cn.mops/R/singlecn.mops.R cn.mops/R/zzz.R
cn.mops/build
cn.mops/build/vignette.rds
cn.mops/data
cn.mops/data/cn.mops.RData
cn.mops/inst
cn.mops/inst/CITATION
cn.mops/inst/doc
cn.mops/inst/doc/cn.mops.R
cn.mops/inst/doc/cn.mops.Rnw
cn.mops/inst/doc/cn.mops.pdf
cn.mops/inst/extdata
cn.mops/inst/extdata/test1.bam
cn.mops/inst/extdata/test1.bam.bai
cn.mops/inst/extdata/test2.bam
cn.mops/inst/extdata/test2.bam.bai
cn.mops/inst/extdata/test3.bam
cn.mops/inst/extdata/test3.bam.bai
cn.mops/man
cn.mops/man/CNVDetectionResult.Rd cn.mops/man/CNVRanges.Rd cn.mops/man/X.Rd cn.mops/man/XRanges.Rd cn.mops/man/calcFractionalCopyNumbers-CNVDetectionResult-method.Rd cn.mops/man/calcFractionalCopyNumbers.Rd cn.mops/man/calcIntegerCopyNumbers-CNVDetectionResult-method.Rd cn.mops/man/calcIntegerCopyNumbers.Rd cn.mops/man/cn.mops.Rd cn.mops/man/cnvr-CNVDetectionResult-method.Rd cn.mops/man/cnvr.Rd cn.mops/man/cnvs-CNVDetectionResult-method.Rd cn.mops/man/cnvs.Rd cn.mops/man/exomeCounts.Rd cn.mops/man/exomecn.mops.Rd cn.mops/man/getReadCountsFromBAM.Rd cn.mops/man/getSegmentReadCountsFromBAM.Rd cn.mops/man/gr-CNVDetectionResult-method.Rd cn.mops/man/gr.Rd cn.mops/man/haplocn.mops.Rd cn.mops/man/individualCall-CNVDetectionResult-method.Rd cn.mops/man/individualCall.Rd cn.mops/man/iniCall-CNVDetectionResult-method.Rd cn.mops/man/iniCall.Rd cn.mops/man/integerCopyNumber-CNVDetectionResult-method.Rd cn.mops/man/integerCopyNumber.Rd cn.mops/man/localAssessments-CNVDetectionResult-method.Rd cn.mops/man/localAssessments.Rd cn.mops/man/makeRobustCNVR.Rd cn.mops/man/normalizeChromosomes.Rd cn.mops/man/normalizeGenome.Rd cn.mops/man/normalizedData-CNVDetectionResult-method.Rd cn.mops/man/normalizedData.Rd cn.mops/man/params-CNVDetectionResult-method.Rd cn.mops/man/params.Rd cn.mops/man/plot.Rd cn.mops/man/posteriorProbs-CNVDetectionResult-method.Rd cn.mops/man/posteriorProbs.Rd cn.mops/man/referencecn.mops.Rd cn.mops/man/sampleNames-CNVDetectionResult-method.Rd cn.mops/man/sampleNames.Rd cn.mops/man/segment.Rd cn.mops/man/segmentation-CNVDetectionResult-method.Rd cn.mops/man/segmentation.Rd cn.mops/man/segplot-CNVDetectionResult-method.Rd cn.mops/man/segplot.Rd cn.mops/man/show.Rd cn.mops/man/singlecn.mops.Rd
cn.mops/src
cn.mops/src/R_init_cnmops.c
cn.mops/src/cn.mops.h
cn.mops/src/cnmops.cpp
cn.mops/src/segment.cpp
cn.mops/vignettes
cn.mops/vignettes/bioinf-article.txi
cn.mops/vignettes/bioinf-bar.png
cn.mops/vignettes/bioinf.cls
cn.mops/vignettes/cn.mops.Rnw
cn.mops/vignettes/cnv.bib
cn.mops/vignettes/natbib.bst
cn.mops/vignettes/natbib.sty

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