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

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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++.

Author
Guenter Klambauer
Date of publication
None
Maintainer
Guenter Klambauer <cn.mops@bioinf.jku.at>
License
LGPL (>= 2.0)
Version
1.20.0
URLs

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.

Files in this package

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