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