cn.mops: cn.mops - Mixture of Poissons for CNV detection in NGS data
Version 1.22.0

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
Bioconductor views CellBiology CopyNumberVariation Genetics HapMap Homo_sapiens Sequencing
Date of publicationNone
MaintainerGuenter Klambauer <cn.mops@bioinf.jku.at>
LicenseLGPL (>= 2.0)
Version1.22.0
URL http://www.bioinf.jku.at/software/cnmops/cnmops.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cn.mops")

Popular man pages

cn.mops: Copy number detection in NGS data.
getReadCountsFromBAM: Calculation of read counts from BAM files.
getSegmentReadCountsFromBAM: Calculation of read counts from BAM files for predefined...
normalizeChromosomes: Normalization of NGS data.
normalizedData-CNVDetectionResult-method: This generic function returns the normalized data of a CNV...
segment: Fast segmentation of CNV calls.
segplot: Visualization of a CNV detection result.
See all...

All man pages Function index File listing

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

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

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/calcFractionalCopyNumbers.R
R/calcIntegerCopyNumbers.R
R/cn.mops.R
R/exomecn.mops.R
R/getReadCountsFromBAM.R
R/getSegmentReadCountsFromBAM.R
R/haplocn.mops.R
R/makeRobustCNVR.R
R/methodsAccess.R
R/normalizeChromosomes.R
R/normalizeGenome.R
R/plot-methods.R
R/referencecn.mops.R
R/segPlot.R
R/segment.R
R/show-methods.R
R/singlecn.mops.R
R/zzz.R
build
build/vignette.rds
data
data/cn.mops.RData
inst
inst/CITATION
inst/doc
inst/doc/cn.mops.R
inst/doc/cn.mops.Rnw
inst/doc/cn.mops.pdf
inst/extdata
inst/extdata/test1.bam
inst/extdata/test1.bam.bai
inst/extdata/test2.bam
inst/extdata/test2.bam.bai
inst/extdata/test3.bam
inst/extdata/test3.bam.bai
man
man/CNVDetectionResult.Rd
man/CNVRanges.Rd
man/X.Rd
man/XRanges.Rd
man/calcFractionalCopyNumbers-CNVDetectionResult-method.Rd
man/calcFractionalCopyNumbers.Rd
man/calcIntegerCopyNumbers-CNVDetectionResult-method.Rd
man/calcIntegerCopyNumbers.Rd
man/cn.mops.Rd
man/cnvr-CNVDetectionResult-method.Rd
man/cnvr.Rd
man/cnvs-CNVDetectionResult-method.Rd
man/cnvs.Rd
man/exomeCounts.Rd
man/exomecn.mops.Rd
man/getReadCountsFromBAM.Rd
man/getSegmentReadCountsFromBAM.Rd
man/gr-CNVDetectionResult-method.Rd
man/gr.Rd
man/haplocn.mops.Rd
man/individualCall-CNVDetectionResult-method.Rd
man/individualCall.Rd
man/iniCall-CNVDetectionResult-method.Rd
man/iniCall.Rd
man/integerCopyNumber-CNVDetectionResult-method.Rd
man/integerCopyNumber.Rd
man/localAssessments-CNVDetectionResult-method.Rd
man/localAssessments.Rd
man/makeRobustCNVR.Rd
man/normalizeChromosomes.Rd
man/normalizeGenome.Rd
man/normalizedData-CNVDetectionResult-method.Rd
man/normalizedData.Rd
man/params-CNVDetectionResult-method.Rd
man/params.Rd
man/plot.Rd
man/posteriorProbs-CNVDetectionResult-method.Rd
man/posteriorProbs.Rd
man/referencecn.mops.Rd
man/sampleNames-CNVDetectionResult-method.Rd
man/sampleNames.Rd
man/segment.Rd
man/segmentation-CNVDetectionResult-method.Rd
man/segmentation.Rd
man/segplot-CNVDetectionResult-method.Rd
man/segplot.Rd
man/show.Rd
man/singlecn.mops.Rd
src
src/R_init_cnmops.c
src/cn.mops.h
src/cnmops.cpp
src/segment.cpp
vignettes
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/cn.mops.Rnw
vignettes/cnv.bib
vignettes/natbib.bst
vignettes/natbib.sty
cn.mops documentation built on May 20, 2017, 9:55 p.m.

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