Package: deepSNV 1.51.0

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_1.51.0.tar.gz
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deepSNV.pdf |deepSNV.html✨
deepSNV/json (API)
NEWS

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

Peer review:

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:
  • HIVmix - Example .bam data and true SNVs.
  • RCC - Example RCC data
  • counts - Example count table
  • phiX - Example phiX data
  • pi - Example prior
  • trueSNVs - Example .bam data and true SNVs.

On BioConductor:deepSNV-1.51.0(bioc 3.20)deepSNV-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

25 exports 1.38 score 71 dependencies 1 dependents 26 mentions

Last updated 2 months agofrom:3d78da12c4

Exports:bam2RbbbbetabinLRTbf2VcfconsensusSequencecontrolcoordinatesdbetabinomdeepSNVestimateDirichletestimateDispersionloadAllDatamakePriormanhattanPlotmcChunknormalizep.combinep.valpbetabinomqvals2VcfrepeatMaskRFshowsummarytest

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsVGAMXMLXVectoryamlzlibbioc

An R package for detecting low frequency variants in deep sequencing experiments

Rendered fromdeepSNV.Rnwusingknitr::knitron Jun 22 2024.

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

Shearwater ML

Inigo Martincorena and Moritz Gerstung

Rendered fromshearwaterML.Rmdusingknitr::rmarkdownon Jun 22 2024.

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

Subclonal variant calling with multiple samples and prior knowledge using shearwater

Rendered fromshearwater.Rnwusingknitr::knitron Jun 22 2024.

Last update: 2016-04-05
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