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
betabinLRT              ShearwaterML
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
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-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
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.
repeatMask              Mask homopolymeric repeats.
show,deepSNV-method     Show method for deepSNV objects
summary                 Summary of a deepSNV object
test                    Get test counts
trueSNVs                Example .bam data and true SNVs.
