# Detection of subclonal SNVs in deep sequencing experiments.

## Documentation for package ‘deepSNV’ version 1.6.0

- 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
consensusSequence | Calculate the consensus sequence.
consensusSequence-method | Calculate the consensus sequence.
consensusSequence-methods | Calculate the consensus sequence.
control | Get control counts
control-method | Get control counts
control-methods | Get control counts
coordinates | Get coordinates
coordinates-method | Get coordinates
coordinates-methods | Get coordinates
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.
deepSNV-methods | 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.
estimateDirichlet-methods | 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.
estimateDispersion-methods | Estimate the Dispersion factor in a beta-binomial model.
Extract | Subsetting for deepSNV objects.
HIVmix | Example .bam data and true SNVs.
manhattanPlot | Manhattan plot.
normalize | Normalize nucleotide counts.
normalize-method | Normalize nucleotide counts.
normalize-methods | Normalize nucleotide counts.
p.combine | Combine two p-values
p.val | Get p-values
p.val-method | Get p-values
p.val-methods | Get p-values
phiX | Example phiX data
plot.deepSNV | Scatter plot of relative nucleotide frequencies.
RCC | Example RCC data
repeatMask | Mask homopolymeric repeats.
repeatMask-method | Mask homopolymeric repeats.
repeatMask-methods | Mask homopolymeric repeats.
RF | Relative frequencies.
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
test-methods | Get test counts
trueSNVs | Example .bam data and true SNVs.
[-method | Subsetting for deepSNV objects.