RCC                     Example RCC data...
RF                      Relative frequencies.
[,deepSNV-method        Subsetting for deepSNV objects.
bam2R                   Read nucleotide counts...
consensusSequence-methods
                        Calculate the consensus sequence.
control-methods         Get control counts...
coordinates-methods     Get coordinates...
deepSNV-class           deepSNV class.
deepSNV-methods         Test two matched deep sequencing experiments
                        for low-frequency SNVs.
deepSNV-package         Estimation of single nucleotide variants from
                        paired deep sequencing experiments
estimateDirichlet-methods
                        Learn a base-specific Dirichlet prior.
estimateDispersion-methods
                        Estimate the Dispersion factor in a
                        beta-binomial model.
manhattanPlot           Manhattan plot.
normalize-methods       Normalize nucleotide counts.
p.combine               Combine two p-values...
p.val-methods           Get p-values...
phiX                    Example phiX data...
plot.deepSNV            Scatter plot of relative nucleotide
                        frequencies.
repeatMask-methods      Mask homopolymeric repeats.
show,deepSNV-method     Show method for deepSNV objects...
summary-methods         Summary of a deepSNV object...
test-methods            Get test counts...
trueSNVs                Example...
