Package: deepSNV 1.59.0

Moritz Gerstung

deepSNV: Detection of subclonal SNVs in deep sequencing data.

This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.

Authors:Niko Beerenwinkel [ths], Raul Alcantara [ctb], David Jones [ctb], John Marshall [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]

deepSNV_1.59.0.tar.gz
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deepSNV_1.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
deepSNV/json (API)

# Install 'deepSNV' in R:
install.packages('deepSNV', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
Datasets:
  • counts - Example count table
  • HIVmix - Example .bam data and true SNVs.
  • phiX - Example phiX data
  • pi - Example prior
  • RCC - Example RCC data
  • trueSNVs - Example .bam data and true SNVs.

On BioConductor:deepSNV-1.59.0(bioc 3.24)deepSNV-1.58.0(bioc 3.23)

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

geneticvariabilitysnpsequencinggeneticsdataimportcurlbzip2xz-utilszlibcpp

6.69 score 1 packages 54 scripts 861 downloads 26 mentions 25 exports 70 dependencies

Last updated from:f250bac75e. Checks:1 ERROR, 13 NOTE, 2 OK. Indexed: yes.

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linux-devel-x86_64NOTE471
source / vignettesOK322
linux-release-arm64NOTE310
linux-release-x86_64NOTE428
macos-release-arm64NOTE223
macos-release-x86_64NOTE753
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macos-oldrel-x86_64NOTE528
windows-devel-arm64NOTE408
windows-devel-x86_64NOTE425
windows-release-arm64NOTE587
windows-release-x86_64NOTE430
windows-oldrel-x86_64NOTE406
wasm-releaseOK142

Exports:bam2RbbbbetabinLRTbf2VcfconsensusSequencecontrolcoordinatesdbetabinomdeepSNVestimateDirichletestimateDispersionloadAllDatamakePriormanhattanPlotmcChunknormalizep.combinep.valpbetabinomqvals2VcfrepeatMaskRFshowsummarytest

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysVariantAnnotationvctrsVGAMXMLXVectoryaml

Shearwater ML
Inigo Martincorena and Moritz Gerstung
Rendered fromshearwaterML.Rmdusingknitr::rmarkdown

Last update: 2016-10-18
Started: 2015-03-09

Subclonal variant calling with multiple samples and prior knowledge using shearwater
1 Introduction | 2 The statistical model | 3 Using shearwater
Rendered fromshearwater.Rnwusingknitr::knitr

Last update: 2016-04-05
Started: 2013-06-25

An R package for detecting low frequency variants in deep sequencing experiments
1 Introduction | 2 Working example | 3 Normalization | 4 Overdispersion | 5 sessionInfo()
Rendered fromdeepSNV.Rnwusingknitr::knitr

Last update: 2013-07-12
Started: 2013-06-25

Readme and manuals

Help Manual

Help pageTopics
Detection of subclonal SNVs in deep sequencing experimentsdeepSNV-package
Read nucleotide counts from a .bam filebam2R
Bayesian beta-binomal test, codename shearwaterbbb shearwater
ShearwaterMLbetabinLRT
Function to create a 'VCF' object with variant calls from an array of Bayes factors.bf2Vcf
Calculate the consensus sequence.consensusSequence consensusSequence,deepSNV-method consensusSequence,matrix-method
Get control countscontrol control,deepSNV-method
Get coordinatescoordinates coordinates,deepSNV-method
Example count tablecounts
Beta-binomial probability distributiondbetabinom
Test two matched deep sequencing experiments for low-frequency SNVs.deepSNV deepSNV,character,character-method deepSNV,character,matrix-method deepSNV,deepSNV,missing-method deepSNV,matrix,character-method deepSNV,matrix,matrix-method
deepSNV class.deepSNV-class
Learn a base-specific Dirichlet prior.estimateDirichlet estimateDirichlet,deepSNV-method estimateDirichlet,matrix-method
Estimate the Dispersion factor in a beta-binomial model.estimateDispersion estimateDispersion,deepSNV,missing-method estimateDispersion,matrix,matrix-method
Helper function for estimating the dispersion factor rhoestimateRho
Subsetting for deepSNV objects.Extract [,deepSNV,ANY,ANY,ANY-method
Function to load all data from a list of bam filesloadAllData
Compute a prior from a COSMIC VCF objectmakePrior
Manhattan plot.manhattanPlot
Little helper function to split the count objects into a smaller digestible chunks and run function FUN on each subsetmcChunk
Normalize nucleotide counts.normalize normalize,deepSNV,missing-method normalize,matrix,matrix-method
Combine two p-valuesp.combine
Get p-valuesp.val p.val,deepSNV-method
Cumulative beta-binomial probability distributionpbetabinom
Example phiX dataphiX
Example priorpi
Scatter plot of relative nucleotide frequencies.plot.deepSNV
Function to create a 'VCF' object with variant calls from an array of q-values.qvals2Vcf
Example RCC dataRCC
Mask homopolymeric repeats.repeatMask repeatMask,deepSNV-method repeatMask,DNAString-method
Relative frequencies.RF
Show method for deepSNV objectsshow,deepSNV-method
Summary of a deepSNV objectsummary summary,deepSNV-method
Get test countstest test,deepSNV-method
Example .bam data and true SNVs.HIVmix trueSNVs