Man pages for deepSNV
Detection of subclonal SNVs in deep sequencing data.

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.