Detection of subclonal SNVs in deep sequencing experiments.

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Documentation for package ‘deepSNV’ version 1.6.0

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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.