deepSNV-package | Estimation of single nucleotide variants from paired deep sequencing experiments |
bam2R | Read nucleotide counts... |
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. |
HIVmix | Example... |
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 | Show method for deepSNV objects... |
show-method | Show method for deepSNV objects... |
summary | Summary of a deepSNV object... |
summary-method | Summary of a deepSNV object... |
summary-methods | Summary of a deepSNV object... |
test | Get test counts... |
test-method | Get test counts... |
test-methods | Get test counts... |
trueSNVs | Example... |
[ | Subsetting for deepSNV objects. |
[-method | Subsetting for deepSNV objects. |