# Detection of subclonal SNVs in deep sequencing data.

## Documentation for package ‘deepSNV’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

deepSNV-package | Detection of subclonal SNVs in deep sequencing experiments
bam2R | Read nucleotide counts from a .bam file
bbb | Bayesian beta-binomal test, codename shearwater
betabinLRT | ShearwaterML
bf2Vcf | Function to create a 'VCF' object with variant calls from an array of Bayes factors.
consensusSequence | Calculate the consensus sequence.
consensusSequence-method | Calculate the consensus sequence.
control | Get control counts
control-method | Get control counts
coordinates | Get coordinates
coordinates-method | Get coordinates
counts | Example count table
dbetabinom | Beta-binomial probability distribution
deepSNV | Test two matched deep sequencing experiments for low-frequency SNVs.
deepSNV-class | deepSNV class.
deepSNV-method | Test two matched deep sequencing experiments for low-frequency SNVs.
estimateDirichlet | Learn a base-specific Dirichlet prior.
estimateDirichlet-method | Learn a base-specific Dirichlet prior.
estimateDispersion | Estimate the Dispersion factor in a beta-binomial model.
estimateDispersion-method | Estimate the Dispersion factor in a beta-binomial model.
estimateRho | Helper function for estimating the dispersion factor rho
Extract | Subsetting for deepSNV objects.
HIVmix | Example .bam data and true SNVs.
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 smaller digestible chunks and run function FUN on each subset
normalize | Normalize nucleotide counts.
normalize-method | Normalize nucleotide counts.
p.combine | Combine two p-values
p.val | Get p-values
p.val-method | Get p-values
pbetabinom | Cumulative beta-binomial probability distribution
phiX | Example phiX data
pi | Example prior
plot.deepSNV | Scatter plot of relative nucleotide frequencies.
qvals2Vcf | Function to create a 'VCF' object with variant calls from an array of q-values.
RCC | Example RCC data
repeatMask | Mask homopolymeric repeats.
repeatMask-method | Mask homopolymeric repeats.
RF | Relative frequencies.
shearwater | Bayesian beta-binomal test, codename shearwater
show-method | Show method for deepSNV objects
summary | Summary of a deepSNV object
summary-method | Summary of a deepSNV object
test | Get test counts
test-method | Get test counts
trueSNVs | Example .bam data and true SNVs.
[-method | Subsetting for deepSNV objects.