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.

AuthorNiko Beerenwinkel [ths], David Jones [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]
Date of publicationNone
MaintainerMoritz Gerstung <mg14@sanger.ac.uk>
LicenseGPL-3
Version1.20.0
http://github.com/mg14/deepSNV

View on Bioconductor

Man pages

bam2R: Read nucleotide counts from a .bam file

betabinLRT: ShearwaterML

bf2Vcf: Function to create a 'VCF' object with variant calls from an...

consensusSequence-methods: Calculate the consensus sequence.

control-methods: Get control counts

coordinates-methods: Get coordinates

counts: Example count table

dbetabinom: Beta-binomial probability distribution

deepSNV-class: deepSNV class.

deepSNV-methods: Test two matched deep sequencing experiments for...

deepSNV-package: Detection of subclonal SNVs in deep sequencing experiments

estimateDirichlet-methods: Learn a base-specific Dirichlet prior.

estimateDispersion-methods: Estimate the Dispersion factor in a beta-binomial model.

estimateRho: Helper function for estimating the dispersion factor rho

Extract-methods: Subsetting for deepSNV objects.

loadAllData: Function to load all data from a list of bam files

makePrior: Compute a prior from a COSMIC VCF object

manhattanPlot: Manhattan plot.

mcChunk: Little helper function to split the count objects into a...

normalize-methods: Normalize nucleotide counts.

pbetabinom: Cumulative beta-binomial probability distribution

p.combine: Combine two p-values

phiX: Example phiX data

pi: Example prior

plot.deepSNV: Scatter plot of relative nucleotide frequencies.

p.val-methods: Get p-values

qvals2Vcf: Function to create a 'VCF' object with variant calls from an...

RCC: Example RCC data

repeatMask-methods: Mask homopolymeric repeats.

RF: Relative frequencies.

shearwater: Bayesian beta-binomal test, codename shearwater

show-deepSNV-method: Show method for deepSNV objects

summary-methods: Summary of a deepSNV object

test-methods: Get test counts

trueSNVs: Example .bam data and true SNVs.

Functions

bam2R Man page
bbb Man page
betabinLRT Man page
bf2Vcf Man page
consensusSequence Man page
consensusSequence,deepSNV-method Man page
consensusSequence,matrix-method Man page
control Man page
control,deepSNV-method Man page
coordinates Man page
coordinates,deepSNV-method Man page
counts Man page
dbetabinom Man page
deepSNV Man page
[,deepSNV,ANY,ANY-method Man page
deepSNV,character,character-method Man page
deepSNV,character,matrix-method Man page
deepSNV-class Man page
deepSNV,deepSNV,missing-method Man page
deepSNV,matrix,character-method Man page
deepSNV,matrix,matrix-method Man page
deepSNV-package Man page
estimateDirichlet Man page
estimateDirichlet,deepSNV-method Man page
estimateDirichlet,matrix-method Man page
estimateDispersion Man page
estimateDispersion,deepSNV,missing-method Man page
estimateDispersion,matrix,matrix-method Man page
estimateRho Man page
Extract Man page
HIVmix Man page
loadAllData Man page
makePrior Man page
manhattanPlot Man page
mcChunk Man page
normalize Man page
normalize,deepSNV,missing-method Man page
normalize,matrix,matrix-method Man page
pbetabinom Man page
p.combine Man page
phiX Man page
pi Man page
plot.deepSNV Man page
p.val Man page
p.val,deepSNV-method Man page
qvals2Vcf Man page
RCC Man page
repeatMask Man page
repeatMask,deepSNV-method Man page
repeatMask,DNAString-method Man page
RF Man page
shearwater Man page
show,deepSNV-method Man page
summary Man page
summary,deepSNV-method Man page
test Man page
test,deepSNV-method Man page
trueSNVs Man page

Files

deepSNV/DESCRIPTION
deepSNV/NAMESPACE
deepSNV/R
deepSNV/R/betabinom.R deepSNV/R/deepSNV-class.R deepSNV/R/deepSNV-experimental.R deepSNV/R/deepSNV-functions.R deepSNV/R/deepSNV-generics.R deepSNV/R/deepSNV-methods.R deepSNV/R/deepSNV-misc.R deepSNV/R/deepSNV-package.R deepSNV/R/shearwater-functions.R deepSNV/R/shearwaterML.R
deepSNV/README.md
deepSNV/build
deepSNV/build/vignette.rds
deepSNV/configure
deepSNV/configure.ac
deepSNV/data
deepSNV/data/HIVmix.RData
deepSNV/data/RCC.RData
deepSNV/data/counts.RData
deepSNV/data/phiX.RData
deepSNV/data/pi.RData
deepSNV/data/trueSNVs.RData
deepSNV/inst
deepSNV/inst/CITATION
deepSNV/inst/NEWS
deepSNV/inst/TODO
deepSNV/inst/doc
deepSNV/inst/doc/deepSNV.R
deepSNV/inst/doc/deepSNV.Rnw
deepSNV/inst/doc/deepSNV.pdf
deepSNV/inst/doc/shearwater.R
deepSNV/inst/doc/shearwater.Rnw
deepSNV/inst/doc/shearwater.pdf
deepSNV/inst/example
deepSNV/inst/example/deepSNV-example.R
deepSNV/inst/example/shearwater-example.R
deepSNV/inst/extdata
deepSNV/inst/extdata/control.bam
deepSNV/inst/extdata/control.bam.bai
deepSNV/inst/extdata/deepSNV.vcf
deepSNV/inst/extdata/shearwater.vcf
deepSNV/inst/extdata/shearwater2.vcf
deepSNV/inst/extdata/shearwaterML.vcf
deepSNV/inst/extdata/test.bam
deepSNV/inst/extdata/test.bam.bai
deepSNV/man
deepSNV/man/Extract-methods.Rd deepSNV/man/RCC.Rd deepSNV/man/RF.Rd deepSNV/man/bam2R.Rd deepSNV/man/betabinLRT.Rd deepSNV/man/bf2Vcf.Rd deepSNV/man/consensusSequence-methods.Rd deepSNV/man/control-methods.Rd deepSNV/man/coordinates-methods.Rd deepSNV/man/counts.Rd deepSNV/man/dbetabinom.Rd deepSNV/man/deepSNV-class.Rd deepSNV/man/deepSNV-methods.Rd deepSNV/man/deepSNV-package.Rd deepSNV/man/estimateDirichlet-methods.Rd deepSNV/man/estimateDispersion-methods.Rd deepSNV/man/estimateRho.Rd deepSNV/man/loadAllData.Rd deepSNV/man/makePrior.Rd deepSNV/man/manhattanPlot.Rd deepSNV/man/mcChunk.Rd deepSNV/man/normalize-methods.Rd deepSNV/man/p.combine.Rd deepSNV/man/p.val-methods.Rd deepSNV/man/pbetabinom.Rd deepSNV/man/phiX.Rd deepSNV/man/pi.Rd deepSNV/man/plot.deepSNV.Rd deepSNV/man/qvals2Vcf.Rd deepSNV/man/repeatMask-methods.Rd deepSNV/man/shearwater.Rd deepSNV/man/show-deepSNV-method.Rd deepSNV/man/summary-methods.Rd deepSNV/man/test-methods.Rd deepSNV/man/trueSNVs.Rd
deepSNV/patches
deepSNV/patches/NAMESPACE.patch
deepSNV/src
deepSNV/src/Makevars
deepSNV/src/Makevars.common
deepSNV/src/Makevars.in
deepSNV/src/Makevars.win
deepSNV/src/bam2R.cpp
deepSNV/src/betabinom.c
deepSNV/vignettes
deepSNV/vignettes/deepSNV.Rnw
deepSNV/vignettes/shearwater.Rnw
deepSNV/vignettes/shearwaterML.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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