deepSNV: Detection of subclonal SNVs in deep sequencing data.
Version 1.22.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorNiko Beerenwinkel [ths], David Jones [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]
Bioconductor views DataImport GeneticVariability Genetics SNP Sequencing
Date of publicationNone
MaintainerMoritz Gerstung <moritz.gerstung@ebi.ac.uk>
LicenseGPL-3
Version1.22.0
URL http://github.com/gerstung-lab/deepSNV
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("deepSNV")

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

BSM Source code
Extract Man page
HIVmix Man page
MASequence Source code
RCC Man page
RF Man page Source code
[,deepSNV,ANY,ANY,ANY-method Man page
bam2R Man page Source code
bbb Man page Source code
betabinLRT Man page Source code
bf2Vcf Man page Source code
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 Source code
deepSNV Man page Source code
deepSNV,character,character-method Man page
deepSNV,character,matrix-method Man page
deepSNV,deepSNV,missing-method Man page
deepSNV,matrix,character-method Man page
deepSNV,matrix,matrix-method Man page
deepSNV-class Man page
deepSNV-package Man page
deepSNVsingle Source code
estimateDirichlet Man page
estimateDirichlet,deepSNV-method Man page
estimateDirichlet,matrix-method Man page
estimateDispersion Man page Source code
estimateDispersion,deepSNV,missing-method Man page
estimateDispersion,matrix,matrix-method Man page
estimateRho Man page Source code
loadAllData Man page Source code
logbb Source code
makePrior Man page Source code
manhattanPlot Man page Source code
mcChunk Man page Source code
mutID Source code
normalize Man page
normalize,deepSNV,missing-method Man page
normalize,matrix,matrix-method Man page
onLoad Source code
onUnload Source code
p.combine Man page Source code
p.val Man page
p.val,deepSNV-method Man page
pbetabinom Man page Source code
phiX Man page
pi Man page
plot.deepSNV Man page Source code
qvals2Vcf Man page Source code
regions2Coordinates Source code
repeatMask Man page
repeatMask,DNAString-method Man page
repeatMask,deepSNV-method Man page
select Source code
shearwater Man page
show,deepSNV-method Man page
significantSNV Source code
summary Man page
summary,deepSNV-method Man page
test Man page
test,deepSNV-method Man page
trueSNVs Man page

Files

DESCRIPTION
NAMESPACE
R
R/betabinom.R
R/deepSNV-class.R
R/deepSNV-experimental.R
R/deepSNV-functions.R
R/deepSNV-generics.R
R/deepSNV-methods.R
R/deepSNV-misc.R
R/deepSNV-package.R
R/shearwater-functions.R
R/shearwaterML.R
README.md
build
build/vignette.rds
configure
configure.ac
data
data/HIVmix.RData
data/RCC.RData
data/counts.RData
data/phiX.RData
data/pi.RData
data/trueSNVs.RData
inst
inst/CITATION
inst/NEWS
inst/TODO
inst/doc
inst/doc/deepSNV.R
inst/doc/deepSNV.Rnw
inst/doc/deepSNV.pdf
inst/doc/shearwater.R
inst/doc/shearwater.Rnw
inst/doc/shearwater.pdf
inst/doc/shearwaterML.R
inst/doc/shearwaterML.Rmd
inst/doc/shearwaterML.html
inst/example
inst/example/deepSNV-example.R
inst/example/shearwater-example.R
inst/extdata
inst/extdata/control.bam
inst/extdata/control.bam.bai
inst/extdata/deepSNV.vcf
inst/extdata/shearwater.vcf
inst/extdata/shearwater2.vcf
inst/extdata/shearwaterML.vcf
inst/extdata/test.bam
inst/extdata/test.bam.bai
man
man/Extract-methods.Rd
man/RCC.Rd
man/RF.Rd
man/bam2R.Rd
man/betabinLRT.Rd
man/bf2Vcf.Rd
man/consensusSequence-methods.Rd
man/control-methods.Rd
man/coordinates-methods.Rd
man/counts.Rd
man/dbetabinom.Rd
man/deepSNV-class.Rd
man/deepSNV-methods.Rd
man/deepSNV-package.Rd
man/estimateDirichlet-methods.Rd
man/estimateDispersion-methods.Rd
man/estimateRho.Rd
man/loadAllData.Rd
man/makePrior.Rd
man/manhattanPlot.Rd
man/mcChunk.Rd
man/normalize-methods.Rd
man/p.combine.Rd
man/p.val-methods.Rd
man/pbetabinom.Rd
man/phiX.Rd
man/pi.Rd
man/plot.deepSNV.Rd
man/qvals2Vcf.Rd
man/repeatMask-methods.Rd
man/shearwater.Rd
man/show-deepSNV-method.Rd
man/summary-methods.Rd
man/test-methods.Rd
man/trueSNVs.Rd
patches
patches/NAMESPACE.patch
src
src/Makevars
src/Makevars.common
src/Makevars.in
src/Makevars.win
src/bam2R.cpp
src/betabinom.c
vignettes
vignettes/deepSNV.Rnw
vignettes/shearwater.Rnw
vignettes/shearwaterML.Rmd
deepSNV documentation built on May 20, 2017, 9:29 p.m.