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.

Author
Niko Beerenwinkel [ths], David Jones [ctb], Inigo Martincorena [ctb], Moritz Gerstung [aut, cre]
Date of publication
None
Maintainer
Moritz Gerstung <mg14@sanger.ac.uk>
License
GPL-3
Version
1.20.0
URLs

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.

Files in this package

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